Use of ape1/ref-1 inhibitors in combination therapies for treatment of cancer

ABSTRACT

Combination therapies including a Apurinic/Apyrimidinic Endonuclease/reduction-oxidation (redox) Factor-1 (APE1/Ref-1) inhibitor specific to inhibit the redox function of APE1/Ref-1 are disclosed herein. The Combination therapies can be used for treating various cancers, as well as other angiogenesis-mediated diseases (e.g., retinal diseases, cardiovascular diseases).

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No.62/473,528 filed on Mar. 20, 2017, and U.S. Provisional Application No.62/521,082 filed on Jun. 16, 2017, which are hereby incorporated byreference in their entireties.

STATEMENT IN SUPPORT FOR FILING A SEQUENCE LISTING

A computer readable form of the Sequence Listing containing the filenamed “IURTC_2017-109-04_ST25.txt”, which is 6,406 bytes in size (asmeasured in MICROSOFT WINDOWS® EXPLORER), is provided herein and isherein incorporated by reference. This Sequence Listing consists of SEQID Nos: 1-33.

BACKGROUND OF THE DISCLOSURE

The present disclosure relates generally to the use of anApurinic/Apyrimidinic Endonuclease/reduction-oxidation (redox) Factor-1(APE1/Ref-1) inhibitor in a combination therapy to treat variouscancers. Particularly, the disclosure relates to the use of APX3330(formerly known as E3330), a highly selective inhibitor of APE1/Ref-I'sredox activity (also referred to herein as “Ref-1”), in a combinationtherapy to treat cancers such as prostate cancer, colon cancer, ovariancancer, bladder cancer, non-small cell lung carcinoma, malignantperipheral nerve sheath tumors, leukemia, as well as otherangiogenesis-mediated diseases (e.g., retinal diseases, cardiovasculardiseases).

Apurinic/Apyrimidinic Endonuclease/reduction-oxidation (Redox) Factor-1(APE1/Ref-1) was originally identified as an endonuclease that plays akey role in the Base Excision Repair (BER) pathway's repair of oxidativeand alkylating damage. Later, APE1/Ref-1 was recognized as a redoxsignaling protein that modulates the activity of certain transcriptionfactors. Since then, additional functions of APE1/Ref-1 have beenuncovered. APE1/Ref-1's duality and pivotal positions in repair andredox activities make it a unique target for therapeutic modulation.

APE1/Ref-1 endonuclease activity is vital to the DNA damage response inall cells, making APE1/Ref-1 a crucial factor in cellular function andsurvival. The repair function has been conserved from E. coli to humans;however, the redox signaling function is observed only in mammals.

APE1/Ref-1 redox signaling affects numerous transcription factorsincluding STAT3, HIF-1α, NF-κB, AP-1, p53, and a few others. APE1/Ref-1redox signaling is a highly regulated process that reduces oxidizedcysteine residues in specific transcription factors as part of theirtransactivation (FIG. 1). APE1/Ref-1 expression is increased in manytumor types, and that change is associated with increased growth,migration, and drug resistance in tumor cells as well as decreasedpatient survival.

Because of the pathways it affects, APE1/Ref-1 is seen as a criticalnode in tumor signaling (FIG. 2), and thus, is a prime target foranticancer therapy However, teasing apart APE1/Ref-1's activities tocreate a specific inhibitor that targets only its endonuclease or redoxfunction is challenging. Particularly, a number of compounds isolatedfrom natural sources have been proposed as Ref-1 redox signalinginhibitors, but none have been shown to directly or specifically inhibitRef-1 redox signaling. An example of these natural compounds,resveratrol, is typical of the other compounds; it's in vivo efficacy issporadic at best due to widely varying bioavailability and low molecularspecificity. Another presumed natural Ref-1 redox inhibitor, curcumin,has been established as a promiscuous compound, interacting with avariety of molecules to give false-positive results in numerousbiological assays. Thus, these are not specific or viable APE1/Ref-1redox inhibitors.

Recently, however, the compound APX3330 (formerly called E3330) has beenidentified as a specific APE1/Ref-1 redox inhibitor. APX3330 has beenextensively characterized as a direct, highly selective inhibitor ofRef-1 redox activity that does not affect the protein's endonucleaseactivity (FIG. 6). Treatment with APX3330 has shown tumor growth andprogression, with limited toxicity, in both in vitro and in vivo models.

It would be advantageous to further evaluate targets such as APE1/Ref-1and rationally design combination therapies, including the correlativebiomarker research, such to provide treatment for cancer patients whosetherapeutic options remain limited. Moreover, it would be furtherbeneficial to identify synthetic combination therapies of two targetswhose co-inhibition leads to dramatic enhancement of cell death comparedto their effect when administered alone.

BRIEF DESCRIPTION

The present disclosure relates generally to the use of selectiveAPE1/Ref-1 inhibitors, APX3330, and compounds derived therefrom (e.g.,APX2009 and APX2014), in a combination therapy to treat various cancers.The combination therapies are found to treat cancers such as prostatecancer, colon cancer, ovarian cancer, non-small cell lung carcinoma,malignant peripheral nerve sheath tumors, leukemia, as well as otherangiogenesis-mediated diseases (e.g., retinal diseases, cardiovasculardiseases).

Accordingly, in one aspect, the present disclosure is directed to acombination therapy comprising an Apurinic/ApyrimidinicEndonuclease/reduction-oxidation (redox) Factor-1 (APE1/Ref-1)inhibitor, wherein the APE1/Ref-1 inhibitor inhibits the redox functionof APE1/Ref-1 and a second therapeutic agent.

In another aspect, the present disclosure is directed to use of acombination therapy for the treatment of cancer, the combination therapycomprising an Apurinic/Apyrimidinic Endonuclease/reduction-oxidation(redox) Factor-1 (APE1/Ref-1) inhibitor, wherein the APE1/Ref-1inhibitor inhibits the redox function of APE1/Ref-1 and a secondtherapeutic agent.

In yet another aspect, the present disclosure is directed to use of acombination therapy for the treatment of retinal disease in a subject inneed thereof, the combination therapy comprising anApurinic/Apyrimidinic Endonuclease/reduction-oxidation (redox) Factor-1(APE1/Ref-1) inhibitor, wherein the APE1/Ref-1 inhibitor inhibits theendonuclease or redox function of APE1/Ref-1 and a second therapeuticagent.

In yet another aspect, the present disclosure is directed to use of acombination therapy for the treatment of a disease selected from thegroup consisting of a cardiovascular disease, bacterial infection,gastric inflammatory disorder, and neurodegenerative disease.

BRIEF DESCRIPTION OF THE DRAWINGS

The disclosure will be better understood, and features, aspects andadvantages other than those set forth above will become apparent whenconsideration is given to the following detailed description thereof.Such detailed description makes reference to the following drawings,wherein:

FIG. 1 depicts the dual functions of APE1/Ref-1. APE1/Ref-1 is amultifunctional protein involved in redox signaling and DNA repair. Theredox signaling function (Ref-1) is responsible for reduction ofoxidized cysteine residues in certain transcription factors (TF's),leading to increased transcriptional activity and upregulation of genesinvolved in cell growth, inflammation, angiogenesis, and other cellularfunctions. The DNA repair function (APE1) is responsible for theendonuclease activity in base excision repair, cutting thephosphodiester backbone of DNA at abasic sites created by glycosylases.These cuts allow the abasic sites to be replaced with appropriatenucleotide bases, completing the DNA base excision repair process.

FIG. 2 depicts Ref-1 signaling as a node in tumor cells and potentialinhibitors in related pathways. Ref-1 redox signaling promotes thetransactivation of transcription factors such as STAT3, HIF-1α, andNF-κB. Inhibiting Ref-1 with APX3330 decreases the expression ofdownstream genes, leading to tumor cell growth arrest and/or death.Additionally, other methods for inhibiting the signaling pathwaysaffected by Ref-1, as well as the enzymes that are upregulated by thesepathways, have been shown to enhance the cytotoxic and cytostaticeffects of Ref-1 inhibition.

FIGS. 3A & 3B depict that dual-targeting of Ref-1 and Jak/STAT signalinginhibits PDAC tumor growth in a 3D co-culture model. FIG. 3A shows Pa03Clow passage patient derived tumor cells grown in 3D cultures in thepresence and absence of CAFs. Spheroids were treated with Ruxolitinibalone and in combination with APX3330 (40 uM), and the area of tumor(red channel) and CAF19#1 (green channel) were quantified following 12days in culture, n=4, fold change refers to comparison of drug-treatedvs media only in the tumor alone spheroids. FIG. 3B depicts theconfirmation of inhibition of STAT3 activation via immunoblotting forpSTAT3 Y705 residue after 4 hours of Ruxolitinib treatment (12.5 uM) inthe 3D assay 8-10 days post plating. Total STAT3 protein is provided asa loading control and reference for the levels of STAT3 in both celltypes. Representative western blot is shown from an n of 3.

FIG. 4 depicts the effects of APE1/Ref-1 in human diseases due to itsmulti-functional nature, APE1/Ref-1 impacts a wide range of humandiseases. Altered expression of Ref-1 affects its regulation of multipletranscriptional factors, leading to various cancers, retinal,cardiovascular, gastric and neurodegenerative diseases. Similarly,modified APE1 DNA repair function affects progression of differentcancers and neurodegenerative diseases.

FIG. 5 depicts that anticancer treatments inducing oxidative DNA damagealters sensory neuronal function. These agents include cisplatin,oxaliplatin, ionizing radiation as well as other drugs. ROS, reactiveoxygen species; Pt, platinum adduct; APE1, apurinic/apyrimidinicendonuclease.

FIGS. 6A-6E depict the differential role of APE1 Redox Inhibition inSensory Neurons vs. Tumor Cells. In tumor cells, Ref-1 redox inhibitionhas multiple downstream effects on tumor growth, survival, migration andtumor inflammation. In sensory neuron cells such as DRG neurons, theaddition of APX3330 does not have a negative effect on the cells andpromotes survival and functional protection through enhancement of Ref-1DNA repair activity against oxidative DNA damaging agents (e.g.cisplatin, oxaliplatin) that invoked the DNA BER pathway (FIG. 6A). Inthe lower right panel, APX3330 attenuates neurotoxicity induced bysystemic administration of cisplatin to tumor-bearing mice. FIG. 6Bdepicts that the treatment paradigm for investigation of the effects ofcisplatin and APX3330 on DNA damage within DRG. Neuroblastoma cells wereimplanted subcutaneously into the right flanks of 6-wk old male NSG miceand allowed to proliferate until tumor volumes ≥150 mm³. Mice were thenrandomized for treatment with cisplatin ±APX3330 treatment. Cisplatinand APX3330 were administered concurrently for 3 weeks (Day 0-Day 17)and endpoints of neuronal toxicity were assessed within the DRG of miceat several time points following the last dose of cisplatin. FIG. 6C arerepresentative blots demonstrating pH2A.X immunoreactivity at D24 andD31. FIGS. 6D & 6E depict quantification of pH2A.X immunoreactivity. Anasterisk indicates statistical significance between D18 and D24 asdetermined by a one-way ANOVA with Tukey's posttest with p<0.05. A crossindicates statistical significance between Veh/Veh group and the Veh/Cis group, as determined by a two-way ANOVA with Bonferroni's posttestwith p<0.05.

FIG. 7 depicts that APX3330 has broad potential in a variety of cancers.Supportive pre-clinical data exists for APX3330 in combination with eachdrug listed in the diagram (second column of boxes from the right) andfor each indication (boxes at far right). *In addition to anti-tumoractivity, APX3330 provides neuroprotection when administered with agentscausing oxidative damage to neurons.

FIGS. 8A-8C depict APE1 expression and batch effects in cells followingsiRNA knockdown. FIG. 8A is a representative Western Blot anddensitometry analysis of Pa03C cells following APE1 knockdown using 20nM siRNA. Vinculin is used as a loading control. siAPE1 samples had 10%APE1 levels in comparison to the SCR control sample. FIG. 8B depictsPrincipal Components Analysis of Uncorrected Gene Expression Data. FIG.8C depicts Principal Components Analysis of Corrected Gene ExpressionData. Following corrections for batch effects using cell cycle-annotatedgenes, the SCR1 and SCR2 groups come together along the x-axis to form asingle SCR group.

FIGS. 9A-9C depict the results of scRNA-seq and comparison of analyses.FIG. 9A is a Violin Plot illustrating the differences in APE1 RNAexpression counts per million (CPM) reads in the SCR, Detectable siAPE1and Undetectable siAPE1 samples. FIG. 9B depicts Mean Expression andFold Change Plot using SCR and siAPE1 cells as the two groups in theanalysis. FIG. 9C depicts Mean Expression and Fold Change Plot usingSCR, detectable siAPE1 and undetectable siAPE1 cells in the analysis.Note that while the analysis uses three separate groups, this plot usesSCR and siAPE1 for calculation of the Mean Expression and Fold Changedue to the limitations of the graph.

FIGS. 10A-10G depict the identification of differentially expressedgenes in relation of APE1 levels. FIG. 10A is a venn diagram showing thethree analyses performed on the scRNA-Seq data and the overlapping genesbetween them. Six genes were significantly changed in all threeanalyses, (FIG. 10B) TMEM45A, (FIG. 10C) TMEM126A, (FIG. 10D) TMEM154,(FIG. 10E) COMMD7, (FIG. 10F) ISYNA1 and (FIG. 10G) TNFAIP2. These genesshow increased changes in expression as APE1 levels are reduced furtherfrom SCR to detectable (but reduced) siAPE1 to undetectable siAPE1.

FIGS. 11A-11C depict overlapping overrepresented canonical pathways.FIG. 11A depicts the 20 most significantly overrepresented pathwaysfollowing IPA analysis on the SCR/detectable siAPE1/undetectable siAPE1results. The x-axis shows the number of genes that were differentiallyexpressed and in the overrepresented pathways. The percentages next tothe pathway labels on the y-axis show the percentage of genes in thepathway which are differentially expressed between SCR and siAPE1 cells.FIG. 11B depicts changes in the EIF2 pathway. The EIF2 pathway was thepathway most affected by APE1 knockdown with 70 DEGs. Genes that aremore highly expressed in siAPE1 cells include eIF5 and eIF4E, whereasthose that are more highly expressed in control cells include eIF2γ,eIF3, GADD34, G-actin, and 40S ribosomal subunit. Genes or complexeswhich were identified as differentially expressed are circled and inbold. FIG. 11C is a heatmap showing changes in expression of DEGs percell involved in the EIF2 pathway. Box showing colors corresponding tonormalized changed in expression shown.

FIGS. 12A-12D depict the validation of scRNA-Seq by qRT-PCR in Pa03Ccells. FIG. 12A depicts genes chosen for qRT-PCR validation followingSCR/siAPE1 validation. FIG. 12B depicts genes statistically significantin all 3 analyses chosen for qRT-PCR validation. FIG. 12C shows theexpression of selected genes assessed via qRT-PCR in Pa03C cells. Thecells were collected after siRNA knockdown and assessed for a reductionin APE1 protein levels of 80% or greater. Each graph is the result of 3independent experiments, showing average fold change in siAPE samplescompared to SCR+/−SD. *p<0.05 (ANCOVA model). FIG. 12D depicts thevalidation analysis. Relation between log 2 fold changes followingscRNA-Seq (x-axis) and qRT-PCR (y-axis). R²=0.82. Linear Regressionanalysis of the slope provided p<0.0001.

FIGS. 13A & 13B depict the effects of Ref-1 in combination withDocetaxel or Trametinib to PDAC cells and CAFs. In FIG. 13B, a higherdose of Docetaxel was used in co-culture due to the decreased potency inthe presence of CAFs.

FIGS. 14A-14C depict 3D spheroid and in vivo combination studies withAPX3330 and Gemcitabine (Gem). Low passage patient derived PDAC cells(Pa03C, FIG. 14A) in co-culture with cancer-associated fibroblasts(CAF19) treated with increasing amounts of Gem in combination withAPX3330 (50 μM). FIG. 14B is a graphical representation: *All Gem+APX330treatments significantly different from Gem alone in tumor (p<0.01).FIG. 14C depicts tumor volume 30 days following treatment. APX3330 (25mg/kg) reduces tumor volume in both PaCa-2 and Panc253 patient derivedcells in animal models as previously published.

FIGS. 15A-15C depict the effect of APX3330 and CPI-613 on the HCT-116cell line.

FIGS. 16A-16D depict the different PDAC cell lines exhibiting variedchanges to expression of select genes following siRNA knockdown.Expression of selected genes assessed via qRT-PCR in (FIG. 16A) Pa02Ccells, (FIG. 16B) Panc10.05 cells and (FIG. 16C) Panc198 cells. Thecells were collected after siRNA knockdown and assessed for a reductionin APE1 protein levels of 80% or greater. Each graph is the result of 3independent experiments, showing average fold change in siAPE samplescompared to SCR+/−SD. *p<0.05 (ANCOVA model). FIG. 16D is a venn diagramshowing the overlapping results of qRT-PCR between the 4 different PDACcell lines. COMMD7, ITGA1, RAB3D and TNFAIP2 were significantly changedin all 4 cell lines. PPIF and SIPA1 were differentially expressed inPa03C, Pa02C and Panc10.05 cells. TAPBP was differentially expressed inPa03C and Panc10.05. PRDX5, ISYNA1, BCRP and NOTCH3 were common betweenPa03C and Pa02C (with BCRP and NOTCH3 changing in opposite directionsbetween the cell lines), while CIRBP was only differentially expressedin Pa03Cs.

FIG. 17 depicts single agent efficacy of parent compound APX3330, aswell as analog compounds APX2009 & APX2014, in 3D spheroid models ofpancreatic cancer. Graphs are means with standard deviations of N=3.

FIG. 18 shows that APX3330 and Napabucasin (BBI-608-STAT3 inhibitor)have synergistic tumor killing in patient-derived 3D spheroid model(Tumor+CAFs) of pancreatic cancer. Concentrations shown are inmicroMolar; Napa 0.125 uM, APX3330 25 or 35 uM, and APX2009 3.5 uM.

FIGS. 19A & 19B show that APX3330 in combination with STAT3i napabucasinin 3D spheroid model (tumor and CAF) had synergistic killing ofpancreatic tumor cells.

FIGS. 20A & 20B show that APX3330 and APX2009 in combination with STAT3inapabucasin in 3D spheroid model (tumor and CAF) demonstratedsynergistic tumor cell killing. Concentrations shown are in microMolar;Napa 0.125 uM, APX3330 25 uM, and APX2009 3.5 uM. **p<0.01, ***p<0.001.

FIGS. 21A & 21B depict dual targeting of Ref-1 and STAT3 results inenhanced killing in genetic PDAC model in vitro (FIG. 21A) and in vivo(FIG. 21B).

FIGS. 22A-22C show that dual-targeting of CA9 and APE1 kills PDAC tumorsin a 3D co-culture pancreatic cancer tumor model.

FIGS. 23A-23E depict combination therapy with APE1/Ref-1 inhibitors in aPDAC 3D co-culture model. FIG. 23A depicts the combination therapy ofAPX3330+Obatoclax (Bcl2 antagonist). FIG. 23B depicts the combinationtherapy of APX3330+Entinostat (HDAC 1 & 3 inhibitor). FIG. 23C depictsthe combination therapy of APX3330+Axitinib (TKI inhibitor). FIG. 23Ddepicts the combination therapy of APX3330+Obatoclax (Bcl2 antagonist).FIG. 23E depicts the combination therapy of APX3330+Entinostat (HDAC 1 &3 inhibitor).

FIGS. 24A-24C depict combination therapy with APE1/Ref-1 inhibitors andCPI-613, a mito targeted TCA cycle inhibitor (FIG. 24A) or STAT3inhibitor, napabucasin (FIGS. 24B & 24C), in a PDAC 3D co-culture model.

FIG. 25 depicts the effects of ruxolitinib in combination with APX3330in a 3D model of pancreatic cancer.

FIG. 26 depicts the effects of ruxolitinib on the phosphorylation ofp-STAT3 (Y705) in the 3D co-culture model of pancreatic cancer.Particularly, the Western blot depicts p-STAT3 (Y705) after 4 hours ofRuxolitinib (12.5 mM).

FIG. 27 depicts the effect of the combination treatment of Rux+APX in aflank co-culture model on tumor growth delay.

FIGS. 28A & 28B depict that combination treatment did not kill the CAFsin the co-cultured tumors.

FIGS. 29A-29G depict the anti-tumor efficacy of APX3330 in combinationwith oxaliplatin.

FIGS. 30A & 30B depict STAT3 inhibitor Napabucasin and Apel redoxinhibitor APX2014 drug combination effects in mouse colon cell lineMC-38.

FIGS. 31A-31E depict PDH and alpha-KDH Metabolic inhibitor CPI-613 andApel redox inhibitor APX3330 synergistic drug combination effects inhuman adenocarcinoma colon suspension cell line Colo-201. FIG. 31Adepicts single agent effects. FIG. 31B depicts combination therapyeffects. FIG. 31C depicts combination EC50 (μM). FIG. 31D depictsChou-Talalay Index of dose combinations. FIG. 31E depicts synergy doses.

FIGS. 32A-32E depict PDH and alpha-KDH Metabolic inhibitor CPI-613 andApel redox inhibitor APX3330 (also referred to herein as E3330)synergistic drug combination effects in human carcinoma colon cell lineHCT-116. FIG. 32A depicts single agent effects. FIG. 32B depictscombination therapy effects. FIG. 32C depicts combination EC50 (μM).FIG. 32D depicts Chou-Talalay Index of dose combinations. FIG. 32Edepicts synergy doses.

FIGS. 33A-33E depict PDH and alpha-KDH Metabolic inhibitor CPI-613 andApel redox inhibitor APX3330 synergistic drug combination effects inhuman carcinoma colon cell line HCT-116. FIG. 33A depicts single agenteffects. FIG. 33B depicts combination therapy effects. FIG. 33C depictscombination EC50 (μM). FIG. 33D depicts Chou-Talalay Index of dosecombinations. FIG. 33E depicts synergy doses.

FIGS. 34A-34E depict PDH and alpha-KDH Metabolic inhibitor CPI-613 andApel redox inhibitor APX2014 synergistic drug combination effects inhuman carcinoma colon cell line HCT-116. FIG. 34A depicts single agenteffects. FIG. 34B depicts combination therapy effects. FIG. 34C depictscombination EC50 (μM). FIG. 34D depicts Chou-Talalay Index of dosecombinations. FIG. 34E depicts synergy doses.

FIGS. 35A-35E depict GLS1 Metabolic inhibitor CB-839 and Apel redoxinhibitor APX3330 synergistic drug combination effects in humancarcinoma colon cell line HCT-116. FIG. 35A depicts single agenteffects. FIG. 35B depicts combination therapy effects. FIG. 35C depictscombination EC50 (μM). FIG. 35D depicts Chou-Talalay Index of dosecombinations. FIG. 35E depicts synergy doses.

FIGS. 36A & 36B depict the effects of a 3-day treatment ofAPX2014+/−cisplatin on the cisplatin resistant bladder cell line,BLCAb001.

FIGS. 37A & 37B depict the effects of a 3-day treatment ofAPX2014+/−cisplatin on the cisplatin resistant bladder cell line,BLCAb002.

FIGS. 38A & 38B depict the effects of APX2014+/−napabucasin on thebladder cell line, T24.

FIGS. 39A & 39B depict the effects of APX2009+/−napabucasin on thebladder cell line, T24.

FIGS. 40A & 40B depict the effects of APX2014+/−napabucasin on thebladder cell line, SCaBER.

FIGS. 41A & 41B depict the effects of APX2009+/−napabucasin on thebladder cell line, SCaBER.

FIGS. 42A-42H depict the importance of the APE1/Ref-1-HIF-1-CA9signaling axis in PDAC cells. FIG. 42A shows the patient-derived PDACtumor cell lines 10.05, Pa02C, and Pa03C, as well as the pancreatic CAFcell line CAF19, exposed to 0.2% oxygen for 24 hours. CA9 protein levelswere compared via western blot (p<0.05 for all cell line differencesbetween normoxia and hypoxia). FIG. 42B shows that LC50 values forSLC-0111 in PDAC cell lines under hypoxic conditions (0.2% O₂) areinversely correlated with CA9 induction in each cell line (R2>0.99).FIG. 42C depicts 10.05 cells grown in monolayer (2D) and cultured innormoxia or 0.2% O₂ for 24 hours and collected for western blotanalysis. 10.05 cells alone or in co-culture with CAF19 cells were grownin 3D cultures for 12 days and collected for western blot analysis.Equal amounts of protein were used from all four samples. CA9 levels in3D cultures alone and with CAFs were 2.5 and 6.2-fold greater(respectively) than in hypoxia-exposed monolayer cultures. FIGS. 42D-42Fshow 10.05 cells transfected with the indicated siRNAs and cultured in3D spheroids. Cells were collected for western blot analysis on D8 toconfirm knock-down (FIG. 42D, p<0.05 for siAPE1/Ref-1 and siCA9 effectson CA9 as well as siAPE1/Ref-1 effects on APE1/Ref-1). Fluorescenceintensity (FIG. 42E) and area (not shown) were measured on days 4, 8,and 12 of 3D culture growth (p<0.001 for differences between knockdowngroups and SC on D12, p<0.05 for difference between siAPE1/Ref-1 andsiCA9 on D12). Representative fluorescent images from each group werecaptured on day 12 (FIG. 42F). FIGS. 42G-42H depict 10.05 cells treatedwith APX3330 and exposed to 0.2% O₂ for 12 hours prior to protein-DNAcross-linking and collection. IPs of HIF1a and a control fornon-specific binding (Rabbit IgG—performed on DMSO+Hypoxia sample) wereperformed using nuclear extracts. qPCR for the HBS-containing region ofthe CA9 promoter was performed. (FIG. 42G, **p<0.01). PCR for theHBS-containing region of the CA9 promoter was performed using IP samplesas well as input DNA (1% of amount loaded into IPs-performed onDMSO+Hypoxia sample) and a negative control (H2O), and these sampleswere detected on a 1% agarose gel with ethidium bromide (FIG. 42H,expected product size=249 bp).

FIGS. 43A-43I depict blockade of CA9 via APE1/Ref-1 or CA9 inhibition.FIGS. 43A & 43B show 10.05 cells treated with APX3330, APX2009, APX2014,and the negative analog RN7-58 and exposed to 0.2% O₂ for 24 hours priorto collection and analysis of CA9 mRNA (FIG. 43A) and protein (FIG. 43B)levels (p<0.01 for differences in CA9 mRNA and protein levels at thehighest concentration tested of each APE1/Ref-1 inhibitor vs. DMSO).FIG. 43C show 10.05 cells cultured in 3D spheroids for 12 days prior tocollection and Western Blot analysis. Cultures were treated with theindicated concentrations of APX3330, APX2009, APX2014, and the negativeanalog RN7-58 on days 4 and 8 (p<0.05 for differences in CA9 expressionat the highest concentration tested of each APE1/Ref-1 inhibitor vs.DMSO). FIGS. 43D & 43E show 10.05 cells transfected with the indicatedsiRNAs or treated with the indicated concentrations of APX2009 orAPX2014 and exposed to 0.2% O₂ for 48 hours. Changes in intracellular pHwere quantified using a pH-sensitive fluorescent dye (pHrodo Redchannel, FIG. 43D), and pH-mediated fluorescence changes were imaged bya blinded third party (FIG. 43E). FIGS. 43F-43I show 3D co-cultures with10.05 (FIGS. 43F & 43H) or Pa03C (FIGS. 43G & 43I) tumor cells (+CAFs)were treated with increasing concentrations of APX3330, APX2009, andAPX2014 (F-G) or SLC-0111 and FC12-531A (FIGS. 43H & 43I) for 12 days,and fluorescence intensity was measured.

FIGS. 44A-44F depict characterization of 3D cultures and effects ofdual-targeting APE1/Ref-1 and CA9. FIGS. 44A-44F depict spheroidsconsisting of 10.05 or Pa03C cells cultured with CAFs for 12 days andcollected for IHC. Slides with sections from these cultures were stainedwith the indicated antibodies/stains. Antibody stains (FIGS. 44B and44D-44F) were counter-stained with hematoxylin. Images are 1,600×magnification.

FIGS. 45A-45R depict APE1/Ref-1 redox signaling inhibition sensitizes 3DPDAC tumor spheroids to CA9 inhibition with second-generationinhibitors. 10.05 and Pa03C cells were plated into 3D cultures withCAF19 cells, and cell growth in these spheroids was measured viafluorescence intensity on days 4, 8, 12, and 16 after plating. Thegrowth of tumor cells vs. CAF cells in the spheroid co-cultures wasassessed separately using different fluorescent labels in the two celltypes. 3D cultures were treated with FC12-531A+APX3330 (FIGS. 45A-45F),APX2009 (FIGS. 45G-45L), or APX2014 (FIGS. 45M-45R) followingmeasurements on days 4, 8, and 12. Fluorescence intensity data withineach experiment were normalized to day 16 DMSO ctrl, and day 16 readingswere compared. Differences between groups were determined using Tukey'smultiple comparisons test: *p<0.05 vs. DMSO; **p<0.01 vs. DMSO;***p<0.001 vs. DMSO; +p<0.05 vs. APE1/Ref-1 Inhibitor; ++p<0.01 vs.APE1/Ref-1 Inhibitor; +++p<0.001 vs. APE1/Ref-1 Inhibitor; ̂p<0.05 vs.FC12-531A; ̂̂<0.01 vs. FC12-531A; ̂̂̂<0.001 vs. FC12-531A. Graphs are meanswith standard deviations of N=3. Fluorescent images of Tumor (redchannel) and CAF (green channel) cells in these spheroids were capturedon day 16.

FIG. 46 is a pathway schematic. APE1/Ref-1 redox signaling contributesto the transactivation of HIF-1 and certain other transcription factors.HIF1α is stabilized under hypoxic conditions, leading to the formationof HIF-1 and subsequent expression of CA9. CA9 coordinates with thebicarbonate transporter and intracellular CAs to stabilize intracellularpH. APE1/Ref-1 redox signaling inhibition (with APX3330, APX2009, orAPX2014) attenuates HIF-1-mediated CA9 expression, sensitizing tumorcells to CA9 inhibition (with SLC-0111 or FC12-531A).

DETAILED DESCRIPTION

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which the disclosure belongs. Although any methods andmaterials similar to or equivalent to those described herein can be usedin the practice or testing of the present disclosure, the preferredmethods and materials are described below.

Cancer

The multi-functional nature of Ref-1 alludes to its expansive roles indisease, particularly cancers. Ref-1 is upregulated in many cancers(Table 1, FIG. 4). This increase is frequently associated withtumorigenesis, cancer aggressiveness, increased angiogenesis,radiotherapeutic and chemotherapeutic resistance, and overall poorprognosis. This makes Ref-1 and the transcription factors it regulatesprime targets for anticancer therapies.

TABLE 1 Tumor tissues/cells with increased Ref-1 expression Cancer withincreased Ref-1 expression Prostate Pancreatic Cervical OvarianOsteosarcoma Germ cell tumor Colon/Colorectal Bladder Head and NeckGastric/Gastro-esophageal Neuroectodermal tumors RhabdomyosarcomasPancreaticobiliary Adult gliomas Non-Small Cell Lung HepatocellularMultiple Myeloma Esophageal Breast Pediatric Ependymoma Melanoma

Prostate Cancer

One of the most widely studied cancers that exhibits Ref-1overexpression is prostate cancer. Overexpression is seenimmunohistologically as a higher percentage of cells staining positivefor Ref-1 in the cytoplasm and an increased intensity of Ref-1 nuclearstaining.

One of the main targets of Ref-1 redox signaling in prostate cancer isSTAT3, which is constitutively active in prostate cancer. STAT3inhibition suppresses prostate cancer cell growth. Conversely, STAT3activation negatively affects overall survival rates and shortensrelapse-free survival (RFS). 95% of metastatic samples taken frompatients who died of castration-resistant prostate cancer were positivefor pSTAT3, with the highest expression seen in bone metastases samples.Collectively, this supports the crucial role of pSTAT3 in prostatecancer aggressiveness and progression.

A downstream target of STAT3 is survivin; its increased expression isalso associated with prostate cancer aggressiveness. mRNA expressionlevels of survivin in prostate biopsy tissues show significantly highersurvivin expression in cancerous tissue, which correlates withhigher-grade cancer and aggressive phenotypes. siRNA knockdown ofsurvivin in prostate cancer cell lines reduces cell proliferation andincreases chemosensitivity to the apoptosis-inducing agent cisplatin.The effects of decreased survivin expression extend in vivo. Miceinjected subcutaneously with siRNA survivin knockdown cells exhibitsignificantly smaller tumors compared with controls.

Interestingly, Ref-1 redox-specific inhibitors APX3330 and APX2009decreased survivin mRNA and protein levels in prostate cancer cells byaffecting NF-κB activity. These inhibitors also reduced cellproliferation. In vivo, APX2009 reduced survivin protein levels and cellproliferation.

Based on the evidence, both STAT3 and survivin present as prime targetsfor anti-prostate cancer therapies. However, to date they have been onlymoderately successful as single-agent therapies. Therefore, thepotential combination of inhibiting both Ref-1 redox function andSTAT3/survivin provides an avenue of targeting both the overarchingregulator and downstream effector of an anti-apoptotic pathway integralto prostate cancer.

In one suitable embodiment, the present disclosure is directed to thecombination of an APE1/Ref-1 inhibitor (5-(2,3-dimethoxy-6-methyl1,4-benzoquinoyl)]-2-nonyl-2-propenoic acid (APX3330),[(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-N,N-diethylpentanamide](APX2009),(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronapthalen-2-yl)methylidene]-N-methoxypentanamide](APX2014)) and a STAT3 inhibitor (e.g., napabucasin) for treatingprostate cancer. In another embodiment, a combination of an APE1/Ref-1inhibitor and a survivin inhibitor (e.g., YM155) for treating prostatecancer is disclosed.

Colon Cancer

Colon cancer, the second leading cause of cancer related death in theU.S., exhibits increased levels of cytoplasmic Ref-1. In liver tumortissue of metastasized colorectal cancer, increased Ref-1 expressioncorresponds to poor patient outcome. In colony-forming assays, siRNARef-1 knockdown significantly increases the sensitivity of colon cancercells to ionizing irradiation (IR). Furthermore, in vivo subcutaneousxenografts also show reduced tumor growth and radiosensitizationfollowing intratumoral Ref-1 siRNA treatment.

The importance of Ref-1 redox signaling in colon cancer is highlightedby the effects that the Ref-1 redox inhibitor APX3330 has on coloncancer stem cells (CCSCs). APX3330 (hereafter referred to as “APX”)significantly reduces CCSC growth in vitro and enhances the cytotoxicityof 5-fluorouracil (5-FU), an anti-metabolite chemotherapeutic. Inxenograft mice injected subcutaneously with CCSCs, intratumoraladministration of APX3330 increases tumor response to 5-fluorouracil(5-FU) delivered intraperitoneally. This indicates that APX3330 couldpotentiate other colon cancer treatments by inhibiting Ref-1's crucialredox activity.

Additionally, as shown below, when APX3330 was combined with CPI-613, alipoate analog known to inhibit the mitochondrial enzymes pyruvatedehydrogenase (PDH) and α-ketoglutarate dehydrogenase (KDGH), there wasa significant killing effect in colon cancer cells.

In one suitable embodiment, the present disclosure is directed to thecombination of an APE1/Ref-1 inhibitor (APX3330, APX2009 and APX2014)and a chemotherapeutic (e.g., 5-FU) for treating colon cancer. Inanother embodiment, a combination of an APE1/Ref-1 inhibitor and aninhibitor of PDH and/or KDGH (e.g., CPI-613) for treating colon canceris disclosed.

Ovarian Cancer

Ref-1 expression in ovarian cancer has been studied widely. Ref-1expression is increased in malignant patient tissue samples, but studiesvary as to the location of this increase.

Some studies show increased expression primarily in the cytoplasm. Inthose studies, cytoplasmic localization of Ref-1 correlates with ovariantumor progression. Additionally, patients with advanced (stage III/IV)cancer have significantly higher Ref-1 expression and lower overallsurvival rates than stage I/II patients. Patients with increasedcytoplasmic Ref-1 are also more resistant to platinatingchemotherapeutics. A different study observed increased Ref-1 nuclearexpression, again with greater increases in stage III/IV compared tostage I/II patients. In other studies, both nuclear and cytoplasmicRef-1 expression were increased, but no correlation was observed betweenRef-1 expression and the cancer stage. Collectively, these studieshighlight that, while Ref-1 expression clearly plays a role in ovariancancer, the heterogeneity of tissue samples makes it hard to discern theroles of Ref-1 nuclear versus cytoplasmic localization.

However, reduced expression of Ref-1 has a clear effect on ovariancancer cells. Ref-1 knockdown in A2780 (nuclear APE1) and CP70(cytoplasmic APE1) cells sensitizes both to cisplatin. In SKOV3 andA2780 cells, Ref-1 siRNA significantly reduces cell proliferation,colony formation, migration and invasion. Similarly, Ref-1 siRNAtreatment of SKOV-3× ovarian cells significantly reduces their growth;the same occurs with APX3330 redox inhibition. Ref-1 siRNA cellsimplanted subcutaneously in mice show markedly reduced growth comparedto control tumors: a 3.2-fold increase in tumor-doubling time (from 5 tomore than 15 days). The tumors also exhibit reduced glucose metabolism.Taken together, a strong case can be made for targeting Ref-1 in ovariancancer as a means to inhibit growth as well as enhance activity of otheranticancer drugs.

Non-Small Cell Lung Carcinoma

Ref-1 has long been considered a prognostic marker in non-small-celllung carcinoma (NSCLC), as Ref-1 protein levels are upregulated inpatient tumor samples. Nuclear Ref-1 expression in tissue samplespresents better survival chances for patients. Cytoplasmic Ref-1 andmRNA expression correlate strongly with poor patient survival andshorter RFS. Both immunohistochemistry and immunoblotting show increasedcytoplasmic and reduced nuclear Ref-1 expression in patients with arecurrence of stage I NSCLC. Post-treatment serum Ref-1 levels areinversely associated with overall survival.

Ref-1 affects platinum-based drugs commonly used in NSCLC. An increasein Ref-1 expression in NSCLC confers resistance to cisplatin treatment,while Ref-1 siRNA knockdown in A549 cancer cells significantly enhancescisplatin cytotoxicity. Patients with tumors not expressing Ref-1respond better to platinum-paclitaxel therapy andcisplatin-docetaxel-gemcitabine treatment, with longer time toprogression and overall survival.

Evidence exists that reducing Ref-1 increases the efficacy of otheranticancer treatments in NSCLC. Decreasing Ref-1 levels in A549 cells invitro and in vivo increases the effectiveness of photodynamic therapy.Ref-1 knockdown with shRNA enhances the anti-tumor activity ofoxymatrine, an alkaloid compound that inhibits proliferation of A549cells.

Collectively, this demonstrates that Ref-1 plays a vital role in NSCLCprogression, and targeting it might lead to better patient outcomes whencombined with various chemotherapeutic treatments.

In one embodiment, the present disclosure is directed to a combinationof an APE1/Ref-1 inhibitor (e.g., APX3330, APX 2009 and APX2014) and achemotherapeutic agent (e.g., paclitaxel, cisplatin, docetaxel,gemcitabine) for treating NSCLC. In another embodiment, a combination ofan APE1/Ref-1 inhibitor and a photodynamic therapy for treating NSCLC isdisclosed.

Malignant Peripheral Nerve Sheath Tumors

Malignant Peripheral Nerve Sheath Tumor (MPNST) is an uncommonneural-origin cancer that can be deadly. Despite much research to date,existing chemotherapeutic agents have not been successful in MPNSTtreatment. Recent research implicates Ref-1 redox targets HIF-1a andparticularly STAT3 in driving MPNST.

Phosphorylated STAT3 expression may indicate aggressive disease atdisease onset. A tissue microarray showed STAT3 expression in primaryMPNST was associated with worse disease-specific overall survival andevent-free survival. In a mouse model of EGFR overexpression, both aJAK/STAT3 inhibitor and STAT3 knockdown by shRNA prevented tumorformation.

In another study, inhibition of STAT3 activation in four MPNST linesresulted in decreased wound healing, cell migration, invasion, and tumorformation. It also reduced HIF-1a expression. Independent shRNA-mediatedHIF-1a knockdown also decreased wound healing, cell migration, invasion,and tumor formation, showing that the STAT3/HIF-1 α signaling pathway isresponsible for tumorigenesis in MPNST.

Furthermore, STAT3's downstream target survivin is amplified in MPNSTs.Survivin is highly expressed in MPNST tissue samples. Survivin knockdownvia siRNA decreases cell growth, inhibits cell cycle progression andincreases apoptosis. Additionally, survivin inhibitor YM155 repressesMPNST xenograft growth and metastasis in vivo.

The role of the STAT3-HIF-1a pathway in MPNST supports the notion ofSTAT3 and/or HIF-1α inhibition as a potential way to treat MPNST.Downstream markers like survivin also present as potential targets.Ref-1 regulates STAT3 as well as HIF-1α; therefore, targeting Ref-1would inhibit multiple targets, providing hope for a viable treatmentfor MPNST. Additionally, the possibility of dual targeting Ref-1 andeither STAT3 or HIF-1α alludes to the potential of completelyeliminating a pathway that is integral to MPNST progression.

In one embodiment, the present disclosure is directed to a combinationof an APE1/Ref-1 inhibitor (e.g., APX3330, APX 2009 and APX2014) and aSTAT3 inhibitor (e.g., napabucasin) for treating MPNST. In anotherembodiment, a combination of an APE1/Ref-1 inhibitor and a HIF-1α fortreating MPNST is disclosed. In yet another embodiment, presentdisclosure is directed to a combination of an APE1/Ref-1 inhibitor and asurvivin inhibitor (e.g., YM155) for treating MPNST.

Leukemia

Few studies have focused on the role of Ref-1 in leukemias. To date theonly published studies have concentrated on the role of Ref-1 in acutepromyelocytic leukemia (APL) and its relationship to all-trans retinoicacid (ATRA, or RA) and retinoic acid receptor (RAR) transcriptionfactors. RAR alpha binds to its DNA binding site (RARE) in aredox-dependent fashion. Studies demonstrate that RAR-RARE binding isblocked through Ref-1 redox inhibition using APX3330. Additionally, theaddition of APX3330 to ATRA increases apoptosis and cellulardifferentiation of APL cells by three-fold. These results indicate thepotential of using APX3330 in combination treatment with ATRA. Thiscould accomplish two things; first, a new treatment combination forleukemias where ATRA is used, and second, a reduction in the ATRA dosewhile maintaining similar or increased therapeutic effect. This latterpoint is important, as one should be able to avoid the toxicity of RAdifferentiation syndrome by being able to increase RA-inducedpromyeloblast differentiation, but with lower amounts of RA. Reducingthe dose of RA has important clinical implications and could help toeliminate some of the undesirable side effects of this therapy, such asdifferentiation syndrome.

Recent studies show Ref-1 is highly expressed in T-cell acutelymphoblastic leukemia (T-ALL). Blockade of Ref-1 by the redox-specificinhibitor APX3330 potently inhibits viability of leukemia T-cells,including primary cells, relapsed and chemotherapy-resistant cells, andcells from a mouse model of T-ALL. Ref-1 redox inhibition promotesleukemia cell apoptosis, which is associated with downregulation ofpro-survival genes. These data demonstrate a role for Ref-1 in theregulation of multiple transcriptional programs in T-cell ALL, andsuggest that disruption of Ref-1 redox function represents an efficientstrategy to target leukemia T-cells, including high-risk, relapsedleukemias.

Finally, investigators studying conversion of pre-leukemic acute myeloidleukemia (AML) cells with TET2 mutations to full-blown AML haveidentified a significant role of Ref-1 in this process. Tet2-deficientstem cells demonstrate resistance to inflammatory challenge as revealedby a higher repopulating and engraftment potential in both primary andsecondary recipients compared to wildtype controls, which, whenstressed, show a remarkable decline in overall engraftment. This processinvokes the NF-κB pathway, which Ref-1 regulates. APX3330 blocks NF-κBfunction, which decreases inflammation and reverses the progression frompre-AML to frank AML in mice bearing AML-associated epigenetic mutationsoften observed in healthy individuals with clonal hematopoiesis. Thesedata suggest that APX3330 treatment could clinically benefit normalindividuals carrying TET2 mutations that show signs of clonalhematopoiesis, as well as patients with TET2 mutations who have acutemyeloid leukemia, myeloproliferative disease and myelodysplasticsyndrome.

In summary, while studies on Ref-1 in leukemia trail behind researchperformed on solid tumors, recent investigations are uncovering acritical role of Ref-1 redox signaling and effectiveness of APX3330 inthose leukemias investigated.

In one embodiment, the present disclosure is directed to a combinationof an APE1/Ref-1 inhibitor (e.g., APX3330, APX 2009 and APX2014) and aNF-κB inhibitor (e.g., napabucasin) for treating T-ALL. In someparticular embodiments, the patient to be treated is carrying TET2mutations that show signs of clonal hematopoiesis.

In some embodiments, the combination of an APE1/Ref-1 inhibitor (e.g.,APX3330, APX 2009 and APX2014) and a NF-κB inhibitor can be used fortreating patients with TET2 mutations who also have acute myeloidleukemia, myeloproliferative disease or myelodysplastic syndrome.

Retinal Diseases

Increased levels of Ref-1 are not limited to cancers (FIG. 4). ElevatedRef-1 has been implicated in age-related cataracts. Ref-1 levels arehigher in the lens epithelium cells of patients versus controls, andRef-1 levels decrease as the opaque degree worsens.

Ref-1 is highly expressed in developing murine retinas, as well asretinal pigment epithelium (RPE) cells, retinal pericytes, choroidendothelial cells (CECs) and retinal vascular endothelial cells (RVECs).Using the Ref-1 inhibitor APX3330 shows that Ref-1 redox activity isrequired for RVEC proliferation, migration and angiogenesis in vitro.Similarly, APX3330 treatment reduced proliferation, migration andangiogenesis in CECs in primate cells in vitro and had an additiveeffect when combined with bevacizumab. RPEs stressed using oxidizedlow-density lipoproteins (oxLDLs) were rescued from proliferationdecline and senescence by APX.

In adult human RPE cell lines, APX3330 reduced the transcriptionalactivity of NF-κB, a key factor associated with inflammation inangiogenesis. It also blocked activation of HIF-1 α and reduced theexpression of its downstream target VEGF. VEGF expression via NF-κB andHIF-1α is primarily responsible for choroidal neovascularization (CNV),a characteristic of neovascular Age-related Macular Degeneration (AMD),also known as wet AMD.

When very low density lipoprotein receptor (VLDLR) knockout mice aretreated with a single intravitreal injection of APX, CNV is reduced.APX3330 also shows anti-angiogenic effects in mice with laser-inducedCNV.

Angiogenesis is also a prime component of other retinal diseases,including Retinopathy of Prematurity (ROP) and Diabetic Retinopathy(DR). Ref-1's redox ability to modulate angiogenesis makes it worthinvestigating in those diseases. Interestingly, both HIF-1α and VEGF areincreased in ROP and DR. Retinal neovascularization, a marker of ROP andDR, is markedly reduced in mice with ischemic retinopathy when treatedwith siRNA targeting HIF-1α or VEGF.

However, the difficulties in creating druggable targets for HIF-1α havebeen discussed. Additionally, ocular anti-VEGF therapies are not alwayseffective and may lead to unwanted side effects. Inhibiting the redoxactivity of Ref-1 may prove to be a more efficacious standalone oradjunctive treatment that can modulate HIF-1α and VEGF in retinaldiseases like wet AMD, ROP and DR.

Other Diseases

Ref-1 has also been shown to play a role in several other diseases.Ref-1's involvement in cardiovascular disease and regulation of bloodpressure is illustrated by aortic coarctation-induced hypersensitive ratmodels showing increased Ref-1 expression levels. Furthermore,heterozygous Ref-1+/−mice exhibit hypertension and diminishedendothelium-dependent vasorelaxation. Ref-1 is part of the SET complexof proteins that are involved in HIV pathogenesis by inhibiting suicidalautointegration. Consequently, knocking down Ref-1 inhibits HIVinfection.

Ref-1 is also implicated in gastric cellular response to Helicobacterpylori (H. pylori) infection. Ref-1 expression levels were elevatedfollowing H. pylori infection in human gastric epithelial cells. H.pylori induced ROS and downstream activated genes were higher in Ref-1deficient cells compared to control, with Ref-1 overexpression reversingthese effects. Additionally, Ref-1 siRNA knockdown inhibited H. pyloriand TNF-α-induced AP-1 and NF-κB DNA binding, as well as IL-8 mRNAexpression and protein secretion in gastric epithelial cells.Collectively, that implicates Ref-1 in gastric inflammatory disorders aswell as sepsis.

Another area of particular interest is neurodegenerative disease (ND).NDs such as Alzheimer's disease (AD), Parkinson's disease (PD),amyotrophic lateral sclerosis (ALS) and cerebral ischemia are allaffected by APE1/Ref-1 dysfunction.

Ref-1 protein levels are elevated in nuclear extracts from themidfrontal cortex and cerebral cortex of AD patients compared tocontrols, with Ref-1 redox activity being seen as a compensatorymechanism for increased oxidative stress. However, reduced APE1endonuclease activity is seen in peripheral blood mononuclear cells ofAD patients, suggesting impaired Base Excision Repair (BER). Thishighlights the different roles that Ref-1 can have within a particulardisease. Similarly, Ref-1 levels are elevated in the central nervoussystem of patients with ALS, a disease exhibiting elevated oxidativestress and DNA damage. In PD, loss of Ref-1 function via gene variantssuggests it is a risk factor, contributing to increased oxidative stressthat leads to loss of dorsal root ganglion (DRG) neurons. Ref-1 isupregulated in cells treated with rotenone and MPP⁺(1-methyl-4-phenylpyridinium), both of which are used to simulate a PDmodel. Ref-1 upregulation protects against neuronal death in thesecells.

After cerebral ischemia, upregulation of Ref-1 protects hippocampalneurons from cell loss and DNA fragmentation. Conversely, transgenicrats with DNA repair-compromised Ref-1 are not protected from ischemicinjury. Ref-1 conditional knockout mice exhibit larger infract volumeand diminished recovery of spatial and cognitive function followingcerebral ischemia.

These findings highlight the wide range of diseases affected by Ref-1,indicating that it is a promising target for treating and managingnumerous diseases.

Combination Therapies

Further, these findings support the use of Ref-1 specific inhibitorssuch as APX3330 and APX2009 in combination therapies with these secondtherapeutic agents. Specifically APX3330 and/or APX2009 can be combinedwith inhibitors of STAT3, HIF1α, CA9, VEGF, NFκB, JAK2, Bcl-2, PTEN,WNT/β-catenin, Endostatin, 5-fluorouracil (5-FU), and a photodynamictherapy (PDT), and the like, and combinations thereof. Moreparticularly, exemplary combinations include APX3330 and/or APX2009 withone or more of a second therapeutic agent selected from those in Tables2 & 3.

TABLE 2 Bortezomib Ispinesib Mesylate SN-38 Topotecan PaclitaxelBryostatin 1 Trametinib LAQ824 Vinblastine BEZ235 PanobinostatMethotrexate Temsirolimus FK866 Afatinib Tozasertib IrinotecanGSK2126458

Suitable dosages of the Ref-1 inhibitor (e.g., APX3330) and secondtherapeutic agent for use in the combination therapies of the presentdisclosure will depend upon a number of factors including, for example,age and weight of an individual, at least one precise cancer/diseaserequiring treatment, severity of a disease, specific Ref-1 inhibitorand/or second therapeutic agent to be combined, nature of a composition,route of administration and combinations thereof. Ultimately, a suitabledosage can be readily determined by one skilled in the art such as, forexample, a physician, a veterinarian, a scientist, and other medical andresearch professionals. For example, one skilled in the art can beginwith a low dosage that can be increased until reaching the desiredtreatment outcome or result. Alternatively, one skilled in the art canbegin with a high dosage that can be decreased until reaching a minimumdosage needed to achieve the desired treatment outcome or result.

Additionally, in some suitable embodiments, the combination therapiescan include pharmaceutically acceptable carriers, for example,excipients, vehicles, diluents, and combinations thereof. For example,where the combination therapies are to be administered orally, they maybe formulated as tablets, capsules, granules, powders, or syrups; or forparenteral administration, they may be formulated as injections(intramuscular, subcutaneous, intramedullary, intrathecal,intraventricular, intravenous, intravitreal), drop infusionpreparations, or suppositories. These compositions can be prepared byconventional means, and, if desired, the active compounds (i.e., APX3330and second therapeutic agent) may be mixed with any conventionaladditive, such as an excipient, a binder, a disintegrating agent, alubricant, a corrigent, a solubilizing agent, a suspension aid, anemulsifying agent, a coating agent, or combinations thereof.

The combination therapies including the Ref-1 inhibitor and secondtherapeutic agent and/or pharmaceutical carriers of the presentdisclosure can be administered to a subset of individuals in need. Inone embodiment, as used herein, an “individual in need” refers to anindividual at risk for or having cancer, and in particular, prostatecancer, breast cancer, ovarian cancer, cervical cancer, osteosarcoma,colon cancer, bladder cancer, pancreatic cancer, gliomas, and the likeas listed in Table 1. In other embodiments, an “individual in need”refers to an individual at risk for or having a retinal disease (e.g.,choroidal neovascularization (CNV), age-related macular degeneration(AMD), retinopathy of prematurity (ROP), diabetic retinopathy (DR)). Inyet other embodiments, an “individual in need” refers to an individualat risk for or having cardiovascular disease, bacterial infection,gastric inflammatory disorders, neurodegenerative diseases (e.g.,Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateralsclerosis (ALS), cerebral ischemia). Additionally, an “individual inneed” is also used herein to refer to an individual at risk for ordiagnosed by a medical professional as having any one of these diseasesand/or disorders. As such, in some embodiments, the methods disclosedherein are directed to a subset of the general population such that, inthese embodiments, not all of the general population may benefit fromthe methods. Based on the foregoing, because some of the methodembodiments of the present disclosure are directed to specific subsetsor subclasses of identified individuals (that is, the subset or subclassof individuals “in need” of assistance in addressing one or morespecific conditions noted herein), not all individuals will fall withinthe subset or subclass of individuals as described herein. Inparticular, the individual in need is a human. The individual in needcan also be, for example, a research animal such as, for example, anon-human primate, a mouse, a rat, a rabbit, a cow, a pig, and othertypes of research animals known to those skilled in the art.

Identification of Additional Pathways for Combinatorial Drug Approach

A proposed factor in the limited success of molecular therapies has beenthe heterogeneity found in tumor samples, especially aggressive onessuch as pancreatic tumors or glioblastomas. This underscores the needfor strategies that target nodal proteins capable of affecting multiplepathways, such as Ref-1. The evaluation of novel targets including Ref-1and rationally designed combination therapy, including correlativebiomarker research, is critical in cancer because therapeutic optionsfor some cancer patients remain limited.

To elucidate increased lethal pairs of chemotherapeutic agents, twogeneral approaches are utilized. They include rational,hypothesis-driven combinations based on the mechanism of action of thecompounds as well as application of “big data” that reveal specific geneexpression profiles or proteomic signatures that would render cancercells vulnerable when used in combination. Combination therapy thatinvolves Ref-1 modulation that results in increased lethality is focusedon herein.

Many studies have investigated the potentiation of DNA-damaging agentsin combination with Ref-1 inhibition. Presumably the predominantmechanism of potentiation in these studies was due to blockade ofRef-1's DNA repair function, which led to cellular inability to respondto the DNA damage caused by the chemotherapeutic agent. Hereinafter,published studies of inhibition of Ref-1 redox function or treatmentwith Ref-1 siRNA (Table 3) are discussed.

Pairing Therapeutic Agents with Ref-1 Based on its Known Functions inCancer Cells

First, a hypothesis-driven approach is used to test chemotherapeuticagents in combination with Ref-1 inhibitors to screen for increasedlethality. This approach involves simultaneously impinging upon Ref-1signaling in conjunction with another key pathway that interacts with ordepends upon Ref-1 function for tumor cell survival. The combination ofthe two should create an increased lethality, dramatically enhancingcell death compared to their effect when administered alone.

TABLE 3 Molecular target/therapeutic agent paired with Ref-1 Pathwaysaffected Model System Doxorubicin Hypoxia/ABC Colon Cancer transporterexpression STAT3 Viability/Migration PDAC Avastin AngiogenesisRetinopathy DNA damage (cisplatin)/Bcl-2 Proliferation/Migration/ NSCLCinhibitor Apoptosis Platinating agents Attenuation of Chemotherapy-(cisplatin/oxaliplatin/carboplatin) vasodilatation of induced neuropathysensory neurons CA9 Hypoxia PDAC WNT/β-catenin ROS/Proliferation PDACEndostatin Angiogenesis Osteosarcoma 5-FU Proliferation/Tumor ColonCancer growth CPI-613 Energy production Colon and Pancreatic pathways;mitochondrial Cancer metabolism pathways Notch3 (γ-secretase inhibitors,Notch signaling Pancreatic Cancer DLL4-inhibiting antibodies) pathway -cell survival, proliferation, differentiation, development, homeostasisRetinoic Acid Differentiation Promyelocytic leukemia PhotodynamicTherapy (PDT) Proliferation/TFAM NSCLC (Transcription Factor A,mitochondria) binding

Using this approach, it was discovered that impinging upon STAT3signaling in combination with Ref-1 signaling dramatically affects theviability and migratory ability of pancreatic cancer cell lines (FIG.3).

Several studies of different cancers support the notion that combinationtherapy involving inhibition of Ref-1 in tumor-promoting processes suchas hypoxia or angiogenesis is efficacious. In an osteosarcoma modelcharacterized by hypoxia and angiogenesis, inhibition of Ref-1 incombination with endostatin demonstrates in vivo efficacy with decreasesin VEGF expression and microvessel density.

Another increased lethal pair involving Ref-1 and hypoxia is thecombination of Ref-1 inhibition with inhibition of the HIF-1α targetCA9. Using pancreatic 3D co-culture models, tumor spheroid area isreduced after dual targeting with Ref-1 and CA9 (FIG. 2). The mechanismof enhancement is believed to be due to an increase in pH and blockadeof the tumor's ability to adapt to hypoxic conditions perpetuatedthrough simultaneous CA9 and Ref-1 blockade.

Finally, studies comparing doxorubicin-sensitive vsdoxorubicin-resistant colon cancer cells demonstrate that hypoxiaenhances the expression of Pgp (P-glycoprotein) and BCRP (breast cancerresistance protein)—and that the addition of APX3330 to doxorubicinunder hypoxic conditions can attenuate HIF activity significantly,blocking the upregulation of Pgp and BCRP. This decrease in Pgp and BCRPexpression may play a role in the observed increase in doxorubicinaccumulation, especially in the parental cells. The results suggestthat, when blockade of Ref-1's redox function blockades HIF signaling,colon cancer cells' response to doxorubicin may be enhanced.

A recent study sought to sensitize NSCLC cell lines to cisplatin bysequential use of AT-101 (gossypol) with cisplatin. AT-101 exerts itsanti-tumor effects in many ways: it is a BH3-mimetic and also has beenshown to inhibit Ref-1's DNA repair and redox activities. Blockade ofthe anti-apoptotic proteins Bcl-2 and Bcl-XL through Ref-1's redoxinhibition of STAT3 activity contributes to the enhanced cell killingand tumor growth seen in this combination. Furthermore, in NSCLC cellline A549, siRNA inhibition of APE1 expression significantly sensitizesA549 cells to cisplatin and increased cell apoptosis. Both of thesestudies point to Ref-1 function as critical in the cells' response tocisplatin, especially in apoptosis signaling through STAT3.

In contrast, a recent study in breast cancer cell lines that wereexposed to cisplatin in combination with inhibitors of either APE1repair or Ref-1 redox activity, cisplatin resistance increased. Theauthors conjecture that a concurrent downregulation of mismatch repairproteins (MSH2, MSH6, MLH1, and ERCC1) may explain why those resultsdiffer from the other studies that demonstrate a greater response tocisplatin when Ref-1 is inhibited concurrently. In the pursuit ofpersonalized medicine, these preclinical studies demonstrate theimportance of elucidating cell-specific signaling following chemotherapyas well as the crosstalk between DNA repair pathways that occursfollowing DNA damaging agents. These factors will need to be consideredas new treatment combinations are proposed, such as considering theaddition of a Ref-1 inhibitor to a cisplatin regimen.

Finally, both Ref-1 inhibition via APX3330 and siRNA knockdown of Ref-1upregulates β-catenin in pancreatic cancer cells. When the WNT/P-catenininhibitor IWR-1 was paired with APX, enhanced cytotoxicity occurred.

These studies show how seemingly “separate tracks” of cancer survivalpathways can intersect, how those intersections involve Ref-1, and theexciting therapeutic possibilities that arise from those intersections.

Mining Big Data to Predict Combination Therapy Involving Ref-1

A second option for uncovering new treatment options is to mine publiclyavailable data sets such as TCGA (The Cancer Genome Atlas) and CCLE(Cancer Cell Line Encyclopedia) to elucidate [in silico] effectivecombination treatments to utilize in cancer treatment settings. The goalis to accelerate the selection of likely increased lethal targets,particularly for aggressive cancers that have few treatment options.

For example, historically in pancreatic cancer, new targeted agentswould be paired with the standard-of-care agent, gemcitabine. But,adding selective inhibitors of multiple cancer-related pathways togemcitabine either did not extend survival significantly or, althoughstatistically significant, did not extend the 5-year survival rate. Intoday's age of omics, “big data” can be used to predict increasedlethality and effective drug combinations rather than a shotgunapproach.

A study combining transcriptional and proteomic profiling followingRef-1 knockdown in HeLa cells reveals several pathways that aredifferentially expressed following Ref-1 modulation. These pathwaysinclude DNA damage, mitochondrial function, and microtubulestabilization. The downregulation of DNA repair proteins following Ref-1knockdown is another confirmation that the addition of a Ref-1 inhibitorto a DNA-damaging agent is deleterious to cancer cells.

The aforementioned study also demonstrates a downregulation inmitochondrial function. Mitochondria are emerging as importantindicators of cellular disease or health following Ref-1 modulation,therefore drugs that target anti-apoptotic mechanisms may be efficaciouswhen combined with Ref-1 inhibition. Such drugs might include Bcl-2inhibitors or YM-155 (a survivin inhibitor). Finally, the proteomicstudy indicates another area in which Ref-1 inhibition may be useful asan increased lethality. Lack of Ref-1 expression affects microtubulestabilization proteins such as actin, impeding proper organization ofthe fibers. Several commonly used chemotherapeutic agents disruptmicrotubule dynamics, including docetaxel, paclitaxel, and vinblastine.Therefore, those agents show promise for being able to be paired withRef-1 inhibition.

Ref-1 DNA Repair and CIPN; Indirect Linking Through Altering RedoxFunction

Chemotherapy-induced peripheral neuropathy (CIPN) is one of the mostprevalent dose-limiting toxicities of anticancer therapy. Up to 90% ofcancer patients experience chemotherapy-induced peripheral neuropathy(CIPN) at some point during or after anticancer treatment. Indeed,anticancer drugs used for the six most common malignancies pose asubstantial risk for CIPN. These drugs include, but are not limited toplatinum agents, taxanes, vinca alkaloids, proteasome inhibitors,immunomodulators and even new, targeted therapeutic agents. There arecurrently no approved treatments to prevent or treat CIPN, thus theneurotoxicity can be dose-limiting for some patients. Platinum drugs,particularly cisplatin and oxaliplatin, are an important component ofnumerous standard-of-care treatment (SOC) regimens for pediatric andadult cancers; for example, oxaliplatin is a part of the FOLFIRINOX andFOLFOX protocols.

CIPN can persist after treatment is completed. Up to 40% of cancerpatients continue to struggle with CIPN five years after treatmentends—and 10% remain symptomatic after more than 20 years. Thus, CIPNdirectly affects cancer survivorship, quality of life, and may limitfuture treatment options if cancer recurs.

In previous studies using an experimental model of cultured sensoryneurons, a causal relationship was established between CIPN and DNAdamage and repair. It was demonstrated that reducing the activity of theDNA base excision repair (BER) pathway by reducing expression of APE1increased the neurotoxicity produced by anticancer treatment, whereas,augmenting the activity of APE1 lessened the neurotoxicity.Additionally, it was demonstrated that APE1's DNA repair function—notthe redox signaling function—is crucial for sensory neuron survival andfunction. It was further demonstrated that the small-molecule redoxinhibitor APX3330 protects sensory neurons from oxidative DNA damagecaused by ionizing radiation (IR), cisplatin, and oxaliplatin (FIG. 5).

This begs the question: how does a Ref-1 redox-specific inhibitor affectDNA repair activity? Although APX3330 is a targeted inhibitor ofAPE1/Ref-1's redox function, it appears that, in the setting of sensoryneurons, it can also enhance the protein's DNA repair (AP endonuclease)activity (FIG. 6). Although this seems counterintuitive, APX3330 causesthe protein to unfold over time. This unfolding primarily alters theamino end of APE1/Ref-1, affecting its interactions with downstreamtranscription factor targets by perturbing the equilibrium of theprotein's folded/unfolded states and facilitating repair activity. Thisdisengagement of APE1 from its Ref-1 redox activity could enhance APE1repair endonuclease activity. When isolated sensory neurons are exposedto APX3330, a concentration-dependent increase in Ref-1 endonucleaseactivity occurs, which is not observed in tumor cells. As discussedherein, it was found that APX3330 protected sensory neurons from DNAdamage and reactive oxygen species (ROS) production induced by agentssuch as ionizing IR, cisplatin and oxaliplatin.

A critical property of any putative therapeutic for neurotoxicity isthat it will not compromise the anticancer function of the treatment(s)administered. Importantly, the enhancement of DNA repair activity byAPX3330 was not observed in mitotic cells. It was shown that APX3330negatively affects the growth and/or survival of tumor cell lines,patient-derived cell lines, and tumors in animal models. Therefore, itis possible that APX3330 could protect postmitotic cells withoutaltering the effects of anticancer drugs on tumor cells (FIG. 6).Additionally, APX3330 does not affect cisplatin or oxaliplatin'stumor-killing efficacy in vivo, yet it protects DRG neurons fromoxidative DNA damage. If further translational research further bearsout these findings, APX3330 could be offered as a neuroprotectivemechanism in humans, facilitating BER repair of oxidative DNA damage andprotecting sensory neurons. In healthy cells, it appears that the DNArepair function—not the redox function of APE1/Ref-1—is necessary forsensory neuronal survival/function. That is opposite from tumor cells.Collectively, these data support the notion that APX3330 can beneuroprotective against cancer therapy without compromising treatment.

Example 1

While a number of studies have investigated genes regulated by APE1, andspecifically its redox signaling function, it has proven difficult tocompile a comprehensive list of genes regulated by APE1 as it isessential for cell viability. Particularly, APE1 knockout in miceresults in embryonic lethality, post-implantation, between days E5-E9.As such, it has not historically been possible to generate stable APE1knockout cell lines.

Approaches to circumvent this dilemma have utilized conditionalknockouts and siRNA knockdowns. While APE1 knockdowns via siRNA areuseful, this approach produces a heterogeneous population, resulting incells with differing amounts of the APE1 protein. Additionally, siRNAknockdowns are transient with APE1 expression recovering over time.Consequently, there may be a limit to the amount of information gainedusing APE1 siRNA in a mixed population.

In order to address this problem and more accurately detect changes tothe potential numerous effectors regulated by APE1, in this Examplesingle-cell RNA Sequencing (scRNA-seq) is utilized to identify newpathways not previously linked to APE1.

Methods

Cell Culture

Pa03C, Pa02C, Panc10.05 and Panc198 (Pa20C) were obtained from Dr.Anirban Maitra at The Johns Hopkins University. All cells weremaintained at 37° C. in 5% CO₂ and grown in DMEM (Invitrogen; Carlsbad,Calif.) with 10% Serum (Hyclone; Logan, Utah). Cell line identity wasconfirmed by DNA fingerprint analysis (IDEXX BioResearch, Columbia, Mo.)for species and baseline short-tandem repeat analysis testing. All celllines were 100% human and a nine-marker short tandem repeat analysis ison file. They were also confirmed to be mycoplasma free.

Transfection with APE1 and Scrambled siRNA

The siRNAs used were Scrambled (SCR) (5′ CCAUGAGGUCAGCAUGGUCUG 3′, 5′GACCAUGCUGACCUCAUGGAA 3′) (SEQ ID NO:1) and siAPE1 (5′GUCUGGUACGACUGGAGUACC 3′ (SEQ ID NO:2), 5′ UACUCCAGUCGUACCAGACCU 3′)(SEQ ID NO:3). All siRNA transfections were performed by plating 1×10⁵cells per well of a 6-well plate and allowing the cells to attachovernight. The next day, Lipofectamine RNAiMAX reagent (Invitrogen,Carlsbad, Calif.) was used to transfect in the APE1 and SCR siRNA atconcentrations between 10 and 50 nM following the manufacturer'sindicated protocol. Opti-MEM, siRNA, and Lipofectamine was left on thecells for 16 hours and then regular DMEM media with 10% Serum was added.Cells were assayed for RNA and protein expression 3 days followingtransfection.

Western Blot Analysis

For whole cell lysates, cells were harvested, lysed in RIPA buffer(Santa Cruz Biotechnology, Santa Cruz, Calif.), and protein wasquantified and electrophoresed. Immunoblotting was performed using thefollowing antibodies: APE1 (Novus Biologicals, Littleton, Colo.) andVinculin (Sigma, St. Louis, Mo.). For qRT-PCR experiments, APE1expression was at least 80% decreased compared to scrambled control inorder to be considered for further analysis.

Single Cell RNA-Sequencing

Three days post-transfection, SCR/siAPE1 cells were collected and loadedinto 96-well microfluidic C1 Fluidigm array (Fluidigm, South SanFrancisco, Calif., USA). All chambers were visually assessed and anychamber containing dead or multiple cells was excluded. The SMARTersystem (Clontech, Mountain View, Calif.) was used to generate cDNA fromcaptured single cells. The dscDNA quantity and quality was assessedusing an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, Calif.,USA) with the High Sensitivity DNA Chip. A total of 48 SCR and 48 siAPE1cells were chosen for sequencing. The Purdue Genomics Facility preparedlibraries using a Nextera kit (Illumina, San Diego, Calif.). Unstranded2×100 bp reads were sequenced using the HiSeq2500 on rapid run mode in 1lane. RNA-seq data are available at the Gene Expression Omnibus (GEO)through accession number pending.

Bioinformatics and Statistical Analyses

Read quality was observed using FastQC v. 0.11.2 and after qualitytrimming was performed using FastX-Toolkit v. 0.0.13.2. A FastXtrimscore of 30 and a trim length of 50 were used. Tophat2 was used toalign trimmed reads to the human genome (ENSEMBL version GrCh38.p7). Onemismatch was allowed. The htseq-count script in HTSeq v.0.6.1 was run tocount the number of reads mapping to each gene. HTSeq used Biopythonv.2.7.3 in the analysis. In order to determine which genes weredifferentially expressed the R package BPSC was used, which isspecifically designed to analyze single-cell RNA-seq data. IngenuityPathway Analysis was utilized in performing network analyses (IPA,QIAGEN Redwood City, www.qiagen.com/ingenuity). An upstream regulatoranalysis, canonical pathway analysis, mechanistic networks analysis,causal network analysis, and downstream effects analysis were performedusing IPA (results were deemed significant for p-values <0.05).Algorithms and details of each type of network analysis are presented inKramer, A., et al., Causal analysis approaches in Ingenuity PathwayAnalysis. Bioinformatics, 2014. 30(4): pp. 523-30.

qRT-PCR Reactions

qRT-PCR was used to measure the mRNA expression levels of the variousgenes identified from the scRNA-seq analysis. Following transfection,total RNA was extracted from cells using the Qiagen RNeasy Mini kit(Qiagen, Valencia, Calif.) according to the manufacturer's instructions.First-strand cDNA was obtained from RNA using random hexamers andMultiScribe reverse transcriptase (Applied Biosystems, Foster City,Calif.). Quantitative PCR was performed using SYBR Green Real Time PCRmaster mix (Applied Biosystems, Foster City, Calif.) in a CFX96 RealTime detection system (Bio-Rad, Hercules, Calif.). The relativequantitative mRNA level was determined using the comparative Ct methodusing ribosomal protein L6 (RPL6) (Pa03C) or Actin (Pancl0.05, Panc 198,Pa02C) as the reference gene. The primers used for qRT-PCR are detailedin Table 4. Experiments were performed in at least triplicate for eachsample. Statistical analysis performed using the 2^(−ΔΔ)C_(T) method andanalysis of covariance (ANCOVA) models.

TABLE 4 Primers used for qRT-PCR. SEQ ID Gene Primer Sequence NO. ActinForward CACCATTGGCAATGAGCGGTTC  4 Reverse AGGTCTTTGCGGATGTCCACGT  5 RPL6Forward ATTGCTTATAGACCGGAAGCCG  6 Reverse AACTTTTTCACCCGCCATCTTG  7BCRP/ Forward GTTCTCAGCAGCTCTTCGGCTT  8 ABCG2 ReverseTCCTCCAGACACACCACGGATA  9 CIRBP Forward GTCAGAGTGGTGGCTACAGTG 10 ReverseGCCCTCGGAGTGTGACTTAC 11 COMMD7 Forward GAGCAGCGAATTGGAGAAAGTGG 12Reverse TCCATCTCGTGCAGGAAGCTGT 13 ISYNA1 Forward GCCAGACCAAAGTCAAGTCCGT14 Reverse CTTAGAGCGGAACTGCAATGGC 15 ITGA1 ForwardCCGAAGAGGTACTTGTTGCAGC 16 Reverse GGCTTCCGTGAATGCCTCCTTT 17 NOTCH3Forward CCAGATGGCTTCACCCCGC 18 Reverse TCAGTTGGCATTGGCTCCAG 19 PPIFForward CGACTTCACCAACCACAATGGC 20 Reverse GGTGTTAGGACCAGCATTAGCC 21PRDX5 Forward TGATGCCTTTGTGACTGGCGAG 22 Reverse CCAAAGATGGACACCAGCGAATC23 RAB3D Forward ACGTGTTGTGCCTGCTGAGGAT 24 ReverseCTTCTCGCAGATGACATCCACC 25 SIPA1 Forward GTGTCCACGATGCTGCCTTACA 26Reverse CTTGCTGCCAGGCTCCTGGAA 27 TAPBP Forward GAGCCTGTTCTCATCACCATGG 28Reverse GTAGGCAAAGCTCAAGTCCAGC 29 TNFAIP2 Forward TGCTCCAGAACCTGCATGAGGA30 Reverse AACTCAGGCAGCCTCGTGTCTA 31

Results

scRNA-Seq Analysis of APE1 Knockdown Cells

The siRNA knockdown of APE1 did not result in complete loss of the APE1protein, as detected by Western blotting, with 10-20% APE1 proteinexpression observed in the siAPE1 samples compared to the scrambledcontrols (SCR) as shown by representative Western blot shown in FIG. 8A.20 nM siRNA was used, as levels greater than this results in off-targeteffects and cell killing not related to APE1 functions. Therefore, inorder to clearly identify changes in gene expression specificallyrelated to the amount of APE1 protein within each individual cell,single-cell RNA-seq was performed on cells following APE1 siRNAknockdown.

Correcting for Batch Effects Using Cell Cycle-Annotated Genes

Due to sample preparation constraints, the siAPE1 and SCR cells weresplit across three batches, with one batch containing siAPE1 and twobatches containing SCR cells (SCR1 and SCR2). Differences between cellbatches were corrected by applying the scLVM R package. In conjunctionwith scLVM, the Biomart R package was used to obtain a list of cellcycle-annotated genes. Specifically, the Gene Ontology (GO) termGO:0007049 was used to identify 189 genes with the annotation name of“cell cycle”. Of these 189 genes, only 102 coincided with the genesremaining in the analysis due to removal of genes exhibiting lowexpression across all cells (gene detection rate quality controlfiltering). A latent variable model was fit to account for cell cycleconfounding, while also incorporating treatment and control covariatesinto the model. Using the fitted latent variable model, it was thenpossible to regress out the cell cycle confounding and compute acorrected dataset.

As an illustration, the plot in FIG. 8B demonstrates the two principalcomponents before correcting for cell cycle and shows that the mostinfluential source of variation (i.e., the x-axis representing 6.84% ofthe total variation) in the data corresponds to the axis along whichSCR1 and SCR2 cells were separated. In contrast, the second mostinfluential source of variation (i.e. the y-axis representing 4.57% ofthe total variation) corresponds to the axis along which siAPE1 and SCRcells were separated.

In the principal components plot following cell cycle correction (FIG.8C), the SCR1 and SCR2 cells showed greater similarity, which resultedin the largest source of variation (i.e., the horizontal axisrepresenting 4.88% of the total variation) now corresponding to the axisalong which the siAPE1 and SCR cells were separated. Using cell cyclecorrection, the variation attributed to cell cycle annotated genes waseffectively removed without removing the variation attributed to thedifferences between siAPE1 treatment and scrambled control. Thus, thelargest source of variation between the cells was attributed to APE1knockdown.

Differential Expression of Genes in the siAPE1 Knockdown and SCR ControlCells

Initially, 48 SCR cells and 48 siAPE1 cells were captured forsequencing. Two SCR and siAPE1 cells each were discarded prior tosequencing due to the presence of multiple cells in the capture site.Cell detection rates (percentage of genes detected in each cell) andgene detection rates (percentage of cells with a given gene expressed)were used for statistical quality control. A threshold of 5% was usedfor both detection rates, resulting in a dataset of 94 cells and 15,351genes. With the median number reads per cell of 0.95 million, the totalnumber of reads per cell was normalized to one million. After theaforementioned cell cycle correction was performed, a further threeoutlier cells were removed as they demonstrated signs of PCR bias withextremely high expression counts for some genes. After all qualitycontrol measures and the removal of outliers, the number of genesdetected per cell averaged 7095.7 using the original (i.e. prior tocorrecting for cell-cycle confounding) gene expression counts. For eachgene, the average number of cells with non-zero gene counts was 42.1using the original gene expression counts.

The average APE1 expression in the remaining 46 cells in the SCR groupwas 101.6 reads per million. Of the siAPE1 cells (n=45), 25 cells had nodetectible APE1 expression with zero APE1 counts. The remaining 20 cellsshowed diminished APE1 expression, with an average of 37.7 reads permillion. A violin plot showing the distribution of the cells in each ofthese groups can be found in FIG. 9A.

While there are many available software packages that are commonly usedfor differential expression analysis, there are important differencesbetween them in terms of what assumptions are made about thedistribution of the count data arising from RNA-seq experiments. Twosuch R packages that use a generalized linear model in order to modelnon-normally distributed data are edgeR and BPSC. The package edgeRmodels the counts with an overdispersed (larger variance) Poissondistribution (also known as the negative-binomial distribution), whichmay not be appropriate for single cell RNA-seq data due the fact thatthere are many more zero counts in this data (a phenomenon referred toas zero-inflation) compared to bulk RNA-seq. The experimental resultsusing edgeR resulted in a large number of differentially expressedgenes, with a potentially high false discovery rate (data not shown).Alternatively, the R package BPSC models the counts in a more flexiblebeta-Poisson distribution that can sufficiently account for thezero-inflation in the single-cell data with the use of additionalparameters in the model. Therefore, the BPSC R package was used in thisExample for the differential expression analysis between SCR cells(n=46) and siAPE1 knockdown cells (n=45).

In order to facilitate comparison of the additional experimental designslater in this Example, the explicit mathematical expression of thelinear component of the generalized model used for the baselinedifferential expression analysis is given by the following:

μ_(ij)=β_(0j)+β_(1j)I[siAPE1]_(i)

where μ_(ij) is the expected value of the beta-Poisson countdistribution of the i^(th) cell for the j^(th) gene, β₀ is the interceptand β₁ is the gene expression in log(Counts per Million). The expressionI[siAPE1]_(i) is an indicator variable that takes the value of one whena cell belongs to the siAPE1 knockdown group. The differentialexpression of the j^(th) gene can then be tested using the null (denotedas H₀) and alternative (denoted as H₁) hypotheses as follows:

H₀:β_(1j)=0

H₁:β_(1j)≠0

While only an expression for the statistical design above is included,it is worth emphasizing that the model is more sophisticated than simplelinear regression, as the distributional assumptions made about the dataare fundamentally different. With this statistical design, the BPSC Rpackage reported 1,950 differentially expressed genes (DEGs) between thesiAPE1 and SCR cells using a false discovery rate cutoff of 5%.

71.7% of these differentially expressed genes had lower expressionlevels in the siAPE1 cells. In comparison, 58.5% of all genes sequencedhad lower expression in the siAPE1 cells, though many of these genes hadvery low expression overall (FIG. 9B). Using Fisher's exact test on thenumber of genes with statistically significant increased/decreasedexpression vs genes with non-significant changes in expression, ap-value of 10-16 was obtained, a highly significant result. Thisindicated that the predominantly inhibitory effect of APE1 knockdown onthe DEGs was greater than any global decrease in expression that may becaused due to external factors (such as cell viability).

Identifying Differentially Expressed Genes in Relation to APE1 Levelswithin the Cell

One of the advantages of performing scRNA-seq is that it allows lookingat APE1 expression in each individual cell. It was therefore possible touse this information to categorize cells within the siAPE1 group ashaving either undetectable APE1 (defined as a cell with zero expressionof APE1) or detectable APE1 (defined as a cell with greater than zeroexpression of APE1). As previously mentioned, within the siAPE1 groupthere were 25 cells with undetectable APE1 (hereafter calledundetectable siAPE1) and 20 cells exhibiting detectable but reduced APE1expression (hereafter called detectable siAPE1).

The delineation of the siAPE1 cells allowed consideration of the SCRcontrol, detectable siAPE1 and undetectable siAPE1 cells as threedifferent categories. Such a model is appropriate if detectable siAPE1cells were considered to be distinct from both undetectable siAPE1 aswell as SCR control cells. The model in this case is given by

μ_(ji)=β_(0j)+β_(1j)[siAPE1]_(i)I[APE1>0]_(i)+β_(2j)I[siAPE1]_(i)I[APE1=0]_(i)

where the expression I[siAPE1]_(i)I[APE1>0]_(i) takes the value of onewhen the i^(th) cell both belongs to the siAPE1 group and has non-zeroAPE1 expression (detectable siAPE1). The expression I[siAPE1]_(i)I[APE1>0]_(i) takes the value of one when the i^(th) cell belongs to thesiAPE1 group and has no detectable expression of APE1 (undetectablesiAPE1). A test for differential expression of the j^(th) gene wasperformed using the null and alternative hypotheses

H₀: β_(1j)=0,δ_(2j)=0

H₁: At least one of β_(1j)≠0 or β_(2j)≠0

This model has two parameters that can be tested for joint significance,whereas the initial SCR/siAPE1 model only had one parameter to test.While it is possible to estimate the joint significance with a singletest of both parameters, the parameter specific significance wascomputed in order to gain insight into the individual differencesbetween undetectable siAPE1 and detectable siAPE1 groups with respect tothe SCR control. In practice, each of these parameters was testedseparately and their joint significance was reported as the resultingp-values using Fisher's method. For two p-values p_(1j),p_(2j)corresponding to test of β_(1j),β_(2j) for the j^(th) gene, the combinedtest statistic is described as

F=−2*log(p _(1j))−2*log(p _(2j))˜×₄ ²

where F is distributed as a chi-squared random variable with fourdegrees of freedom under the null hypothesis. The combined p-value p* istherefore computed as

p*=1−P×₄ ²(F<F)

where Pχ₄ ² denotes the cumulative distribution function of a χ₄ ²random variable and F* is the empirical test statistic computed similarto F above, only using the computed p-values for each gene. It is worthmentioning that Fisher's method, as described above, does not enforcethe assumption of a consistent direction of differential expression ofthe two groups when compared to the control. While it may be useful toincorporate the assumption that the direction (positive or negative) ofdifferential expression should be consistent among the detectable andundetectable siAPE1 groups directly into the statistical design of theanalysis, these ideas were not pursued further.

This analysis allows for detection of differences that may be presentbetween SCR and detectable siAPE1 cells, between SCR and undetectablesiAPE1 cells, or between SCR and both categories of siAPE1 cells. Thejoint analysis guards against a single outlier preventing a gene frombeing reported as differentially expressed as one parameter may bereported as insignificant, but not the other. Additionally, since thedirection of the expression change of the DEGs is expected to beconsistent as one moves from the SCR group to the detectable siAPE1group to undetectable siAPE1 group, this experimental design aids in theinterpretation of results and helps to identify genes potentiallyaffected by outliers. This SCR/detectable siAPE1/undetectable siAPE1analysis identified 2,837 genes using a false discovery rate of 5%. Ofthe 1,950 DEGs identified in the SCR/siAPE1 analysis, 1,945 (99.7%) werefound to be differentially expressed in this subsequent analysis.Additionally, 72.1% of the DEGs were down-regulated (FIG. 9C), similarto the 71.7% down-regulated in the SCR/siAPE1 analysis. This consistencyindicated that the increase in number of DEGs identified was due to themore rigorous statistical model, making it the preferable analysis.

Analysis was also performed to investigate which genes weredifferentially expressed between the detectable and undetectable siAPE1cells. This analysis was statistically underpowered due to the smallersample size of the two cell groups. It resulted in only 60 DEGs beingidentified, indicating that the detectable and undetectable siAPE1 cellshad similar gene expression patterns, especially when compared to theSCR control cells. When comparing the DEGs to the SCR/detectablesiAPE1/undetectable siAPE1 results, 42 genes were found to overlap,while only six genes overlapped with the SCR/siAPE1 analysis (FIG. 10A).These six genes (TMEM45A, TMEM126A, TMEM154, COMMD7, ISYNA1 and TNFAIP2)were the only genes overlapping between all three analyses. Violin plotsillustrating the expression of these genes in relation to APE1expression per cell are shown in FIGS. 11B-11G. The presence of thesesix genes in all three analyses confirmed that, as APE1 levels decrease,the expression levels of these six genes changed further.

Determining the Clinical Relevance of the Differentially Expressed Genes

One overarching objective of this Example was to ascertain potentialcombinations of APE1 inhibition with clinically approved drugs thatimpinge on pathways impacted by altered APE1 expression, initially inpancreatic cancer, but eventually in other cancers. Toward this goal,the clinical relevance of the DEGs identified by the different analyseswas investigated using The Cancer Genome Atlas (TCGA), which containsdata such as tumor gene expression and clinical outcomes from cancerpatients. Due to the small number of DEGs identified in the detectablesiAPE1/undetectable siAPE1 analysis, it was excluded from this TCGAanalysis. Both the SCR/siAPE1 and SCR/detectable siAPE1/undetectablesiAPE1 analyses were utilized. Performing this TCGA analysis allowed formeasurement of the clinical relevance of the DEGs identified in thisExample, and also provided a performance metric for the two analyses.

The RTCGA toolbox was used to analyze the data from the TCGA. In thisanalysis, a gene is defined as clinically relevant if its expressionlevel at the time of sequencing is statistically significantly relatedto the number of days until death in patients with pancreatic cancer.The statistical significance of a gene is determined using the Coxproportional hazards regression model, a commonly used model in clinicaltrials and biostatistics. Specifically, the outcome of days until death(accounting for censoring due to a patient still being alive at the timeof sequencing) was regressed on the normalized gene expression data ofpatient tumor samples via bulk RNA-Seq using the R package survival.Only expression levels in the analysis were used, modeling one gene at atime across all tumor types and stages. In all, 178 patient tumorsamples were included and a total of 20,501 genes were considered. Dueto naming conventions and quality control procedures, only 10,292 werein common between the total number of genes sequenced in the scRNA-seqanalysis and the TCGA analysis of survival outcomes. Therefore, for thisanalysis, the discussion will be limited to only these 10,292 genes. Forthis reason, the total number of differentially expressed genes reportedbelow for both differential expression analyses are fewer than reportedin previous sections.

The TCGA analysis resulted in 1,627 genes statistically significantlyrelated to time until death using a false discovery rate of 5%. Of the1,486 DEGs considered from the SCR/siAPE1 analysis, 246 genes (16.6%)were found to be clinically relevant. The SCR/detectablesiAPE1/undetectable siAPE1 analysis identified 345 clinically relevantgenes (16.3%) out of the available 2,115 DEGs.

The SCR/detectable siAPE1/undetectable siAPE1 analysis identified moreDEGs that are clinically relevant without a change in the overallpercentage of clinically relevant genes. This further illustrates thatthe 856 genes unique to the analysis were not statistical anomalies, butauthentic results identified due to a more stringent statistical model.Because of this result, all following analyses were carried out usingthe SCR/detectable siAPE1/undetectable siAPE1 results.

Gene Expression Patterns in Cancer-Related Pathways

Ingenuity pathway analysis (IPA) was used to determine pathwaysregulated by APE1 based on the DEGs previously identified in theSCR/detectable siAPE1/undetectable siAPE1 analysis. Full pathwayanalysis results are in Table 5. A total of 104 canonical pathways wereidentified as overrepresented using a one-tailed Fisher's exact test.Data presented in FIG. 11A demonstrate the 20 most statisticallysignificant overrepresented pathways, six of which were previouslyunlinked to APE1. The EIF2 signaling pathway (p-value=1.58×10−18) with70 DEGs was found to be the pathway most affected by APE1 knockdown. Anoverview of the pathway with the genes that were affected is presentedin FIG. 11B, with a heatmap highlighting the 70 DEGs and theirexpression in each cell shown in FIG. 11C. Other previously unlinkedpathways were the mTor pathway (p-value=3.98×10−12) with 55 DEGs and theregulation of eIF4 and p7056K signaling pathway (p-value=3.63×10−9) with42 DEGs. These pathways, along with the virus entry via endocyticpathway, regulation of Actin-based motility by Rho and putrescinedegradation pathways, are now putatively linked to APE1 based on thescRNA-seq data, expanding APEI's already diverse role within the cell.In total, 44 pathways previously unassociated with APE1 were identifiedin this Example. These results highlight the importance of single cellRNA-seq in determining clear gene expression and pathway interactions.

TABLE 5 Complete results of IPA Pathway analysis. Ingenuity CanonicalPathways p-value EIF2 Signaling  1.58 × 10⁻¹⁸ mTOR Signaling  3.98 ×10⁻¹² Regulation of eIF4 and p7056K Signaling 3.63 × 10⁻⁹ MitochondrialDysfunction 8.12 × 10⁻⁶ Oxidative Phosphorylation 1.02 × 10⁻⁵Sumoylation Pathway 2.63 × 10⁻⁵ Aldosterone Signaling in EpithelialCells 1.41 × 10⁻⁴ ILK Signaling 3.71 × 10⁻⁴ Huntington's DiseaseSignaling 4.07 × 10⁻⁴ Virus Entry via Endocytic Pathways  5.5 × 10⁻⁴Apoptosis Signaling  5.5 × 10⁻⁴ Protein Kinase A Signaling 5.89 × 10⁻⁴Protein Ubiquitination Pathway 7.08 × 10⁻⁴ Glycolysis I 7.41 × 10⁻⁴ CDK5Signaling 9.12 × 10⁻⁴ NADH Repair 0.001 Putrescine Degradation III 0.001Androgen Signaling 0.001 Regulation of Actin-based Motility by Rho 0.002Aryl Hydrocarbon Receptor Signaling 0.002 Mitotic Roles of Polo-LikeKinase 0.002 Phospholipase C Signaling 0.002 Role of CHK Proteins inCell Cycle Checkpoint Control 0.003 GÎ ± q Signaling 0.003 PI3K/AKTSignaling 0.003 ERK/MAPK Signaling 0.003 Spermine and SpermidineDegradation I 0.004 Synaptic Long Term Potentiation 0.005Caveolar-mediated Endocytosis Signaling 0.005 Integrin Signaling 0.005fMLP Signaling in Neutrophils 0.005 RAR Activation 0.006 HIF1Î ±Signaling 0.006 Pyrimidine Deoxyribonucleotides De Novo 0.006Biosynthesis I IL-17A Signaling in Fibroblasts 0.007 Unfolded proteinresponse 0.007 NRF2-mediated Oxidative Stress Response 0.007 Productionof Nitric Oxide and Reactive Oxygen Species 0.007 in Macrophages BreastCancer Regulation by Stathmin1 0.009 3-phosphoinositide Degradation0.009 Cell Cycle: G2/M DNA Damage Checkpoint Regulation 0.009 ActinNucleation by ARP-WASP Complex 0.01 Pyrimidine RibonucleotidesInterconversion 0.01 DNA Double-Strand Break Repair by Non-Homologous0.01 End Joining Glycogen Degradation III 0.01 Guanine and GuanosineSalvage I 0.01 Adenine and Adenosine Salvage I 0.01 Glioma InvasivenessSignaling 0.01 Ethanol Degradation II 0.011 Tryptophan Degradation X(Mammalian, via Tryptamine) 0.011 Ethanol Degradation IV 0.011 GNRHSignaling 0.011 14-3-3-mediated Signaling 0.012 FcÎ³ Receptor-mediatedPhagocytosis in Macrophages 0.012 and Monocytes Antigen PresentationPathway 0.012 LPS-stimulated MAPK Signaling 0.013 p70S6K Signaling 0.013Pyrimidine Ribonucleotides De Novo Biosynthesis 0.014 ATM Signaling0.015 Oxidative Ethanol Degradation III 0.016 Endoplasmic ReticulumStress Pathway 0.016 Insulin Receptor Signaling 0.016 CXCR4 Signaling0.017 RhoGDI Signaling 0.017 Noradrenaline and Adrenaline Degradation0.018 nNOS Signaling in Neurons 0.018 Signaling by Rho Family GTPases0.018 Tight Junction Signaling 0.019 PI3K Signaling in B Lymphocytes0.020 IL-3 Signaling 0.020 D-myo-inositol-5-phosphate Metabolism 0.022Role of Tissue Factor in Cancer 0.023 Superpathway of Inositol PhosphateCompounds 0.023 PPAR Signaling 0.026 Cholecystokinin/Gastrin-mediatedSignaling 0.027 Xenobiotic Metabolism Signaling 0.027 CeramideBiosynthesis 0.027 Glycogen Degradation II 0.027 Assembly of RNAPolymerase II Complex 0.028 Sonic Hedgehog Signaling 0.029 D-glucuronateDegradation I 0.029 Germ Cell-Sertoli Cell Junction Signaling 0.029Hypoxia Signaling in the Cardiovascular System 0.031 Salvage Pathways ofPyrimidine Ribonucleotides 0.031 Hereditary Breast Cancer Signaling0.031 UVB-Induced MAPK Signaling 0.034 Growth Hormone Signaling 0.034Estrogen Receptor Signaling 0.036 Role of IL-17A in Psoriasis 0.036 BCell Receptor Signaling 0.037 Axonal Guidance Signaling 0.037 HistamineDegradation 0.038 Fatty Acid Î²-oxidation I 0.039 Thrombin Signaling0.041 tRNA Charging 0.041 RhoA Signaling 0.042 Phagosome Formation 0.042Endothelin-1 Signaling 0.042 Molecular Mechanisms of Cancer 0.042Neurotrophin/TRK Signaling 0.043 Agrin Interactions at NeuromuscularJunction 0.046 Retinol Biosynthesis 0.047 AMPK Signaling 0.047 TheVisual Cycle 0.047

A number of the significant pathways affected by APE1 knockdown confirmprevious observations and therefore provided validation for the results.For example, the HIF1α signaling pathway, shown to be regulated by APE1,was found to be significantly down-regulated in the pathway analysis(p-value=0.006). Similarly, the mitochondrial dysfunction(p-value=8.12×10-6) and Huntington's disease signaling(p-value=4.07×10-4) pathways are both in the top ten significantlyoverrepresented pathways affected by APE1 knockdown. The mitochondrialdysfunction pathway has 37 DEGs, while there are 42 DEGs in theHuntington's disease signaling pathway. Mitochondrial dysfunction isbelieved to play a role in Huntington's disease pathology, and priorstudies have demonstrated that APE1 is important for the maintenance ofmitochondrial function. APE1 is also known to participate inmitochondrial DNA repair functions. While APE1 is known to influencethese pathways, this Example expands the understanding of APE1 withinthe cell by implicating the genes in the pathways that are affected byAPE1 knockdown.

Validating scRNA-Seq Results Using qRT-PCR

The scRNA-seq results of the SCR/siAPE1 analysis were validated byperforming qRT-PCR in Pa03C cells following siRNA knockdown. A panel ofgenes, from distinct pathways and showing varying changes followingknockdown, was chosen (FIG. 12A). These genes were present in both theSCR/siAPE1 and SCR/detectable siAPE1/undetectable siAPE1 analyses.Efficiency of siRNA knockdown was assessed using Western blots, withonly samples exhibiting greater than 80% reduction in APE1 expressioncompared to the scrambled controls chosen.

In addition, validation of 3 genes that were differentially expressedand statistically significant in all analyses (SCR/siAPE1, DetectablesiAPE1/undetectable siAPE1 and SCR/detectable siAPE1/undetectablesiAPE1) was performed. The presence of these genes (FIG. 12B) within all3 analyses indicates that their expression changes more dramaticallywith greater APE1 knockdown.

The genes that showed statistically significant increased or decreasedexpression in scRNA-seq exhibit changes in the same direction followingqRT-PCR (FIG. 12C), with a decrease seen in the mRNA levels of CIRBP,COMMD7, ISYNA1, ITGA1, NOTCH3, PRDX5, RAB3D, SIPA1, TAPBP and TNFAIP2.The expression of BCRP and PPIF was significantly increased followingknockdown. The fold changes from scRNA-seq were plotted against qRT-PCRfold changes in FIG. 12D. With an R² value of 0.82 and p<0.0001 (LinearRegression analysis), it was confirmed that the fold changes wereconsistent and validated the single-cell scRNA-seq studies.

Additionally, the “connectivity map” project compared the query geneexpression signatures against a database of gene expression profilesderived from treating human cells with various agents to identifysimilarities and predict drug mechanisms. Incorporating drug sensitivitydata of cell lines with similar gene expression profiles were used topredict effective combination treatments. Cancer Cell Line Encyclopedia(CCLE, https://portals.broadinstitute.org/ccle/home) contains baselinegene expression data of 1,036 cancer cell lines and pharmacologicprofiles (IC₅₀, AUC) for anticancer drugs across 504 cell lines. CCLEgene expression profile set as the reference was used, as well as datafrom Genomics of Drug Sensitivity in Cancer (GDSC) and CancerTherapeutics Response Portal (CTRP,http://portals.broadinstitute.org/ctrp/). Gene expression of CCLE celllines and of Ref-1 knockdown single cells were normalized and ranked. Ahigh correlation indicated that a drug that is effective in a CCLE cellwill have relatively high probability of being effective in a cell whoseRef-1 signaling is inhibited. After identifying the CCLE cell lines withsignificantly high correlations with Ref-1 single cells(correlation >0.5), the frequency of these drugs that have high potency(IC₅₀<1 μM) on these CCLE cell lines was counted. Using thiscomputational screening strategy, Table 6 lists drugs that are predictedto be most effective with Ref-1 inhibition, in order of the drugs thathad the greatest number of cell lines. The agents in Table 6 will beutilized in combination treatments with APX3330 for further analysis.

TABLE 6 List of compounds likely to synergize with APX3330 based on CCLEand single cell RNAseq Class of drug P value HDAC inhibitorsPanobinostat 2.60E−07 Entinostat 1.00E−06 Vorinostat 1.87E−06 Merck601.13E−10 Apicidin 2.31E−08 BRD-K66532283 2.16E−07 Nucleoside analogsDecitabine 4.97E−09 Gemcitabine 4.20E−07 Clofarabine 1.83E−06 Ara-C6.36E−08 DNA damaging agents Doxorubicin 1.66E−10 Etoposide 5.42E−07Topotecan 8.36E−07 Bendamustine 1.18E−06 Dacarbazine 1.66E−06 MitomycinC 6.78E−06 Chlorambucil 6.65E−06 RTKi (Receptor tyrosine Axitinib3.32E−09 kinases) Sunitinib 4.91E−09 KW-2449 9.39E−09 MGCD-265 3.46E−07Imatinib 5.93E−07 Pazopanib 2.65E−07 BRDi (Bromodomain) I-BET1516.99E−09 GSK525762A 9.65E−08 JQ-1 1.48E−07 Jak2 NVP-BSK805 1.50E−07Momelotinib 3.29E−07 Tubulin polymerization Vincristine 7.59E−08 CHM-14.05E−07 PLKi (Polo-like kinase) GSK461364 6.66E−08 BI-2536 9.46E−07Mdm2i Serdemetan 1.11E−06 HLI 373 6.22E−06 S1Pi FTY720 1.46E−06

Example 2

In this Example, Ref-1 inhibition in combination with docetaxel andtrametinib was analyzed.

Standard 3D co-culture assays as prepared in Arpin, C. et al., MolCancer Ther 15, 794-805 (2016); Logsdon, P. et al., Mol Cancer Ther 15,2722-2732 (2016); Cardoso, A. et al., PloS one 7, e4742 (2012); andKelley, M. et al., The Journal of pharmacology and experimentaltherapeutics 359, 300-309 (2016) were used to evaluate the cytotoxicityof the combinations on tumor cells as well as cancer-associatedfibroblasts.

As shown in FIG. 14, Ref-1 inhibition in combination with docetaxel andtrametinib was shown to be more effective than either agent alone.Docetaxel was chosen because it was gave the highest number of CCLE celllines (115 lines) that were likely to synergize with Ref-1 inhibition;Trametinib was chosen due to the prevalence of PDAC lines (14%) in theCCLE lines revealed from the computational screening strategy.

Example 3

In this Example, inhibition of Ref-1 via APX3330 in combination withgemcitabine was analyzed.

Standard 3D co-culture assays as described in Example 2 were used toevaluate the cytotoxicity of the combination on tumor cells as well ascancer-associated fibroblasts.

The scientific premise of this approach is based on: 1) a computationalapproach providing chemotherapeutic agents to partner with APX3330 thatresult in augmented effects on PDAC killing; and 2) 3D and in vivostudies with APX3330 and gemcitabine demonstrating that addition ofAPX3330 increased the effects of gemcitabine. In the 3D spheroid model(FIGS. 14A & 14B), it was demonstrated a dose-dependent combinationeffect of gemcitabine and APX3330 on a patient-derived tumor line, Pa03Cin co-culture with CAFs. There was a reduction in the area of the CAFswith APX3330 alone, but the effects were not enhanced with the additionof gemcitabine (See green bars, FIG. 14B).

Additionally, the beneficial effects of combining APX3330 withgemcitabine in vivo were demonstrated (FIG. 14C). APX3330 (25 mg/kg) wascombined with a standard dose of gemcitabine (35 mg/kg) to demonstratethe “additive” effects of APX3330 in reducing pancreatic tumor volumes.The data in FIG. 14C is tumor volume at sacrifice. Combination therapywas well-tolerated. There was a significantly decreased tumor volume inthe combination treatments of APX3330 with gemcitabine compared to thesingle agents alone. All treatments, single or combination weresignificantly different from the vehicle control. These data demonstratea novel combination effect when APX3330 is combined with gemcitabine ina xenograft model as well as lend support to the interrogation ofcombination therapy with APX3330 and the FDA approved agents in Table 6.

Example 4

In this Example, the inhibition of Ref-1 via APX3330 in combination withthe PDH/KDGH inhibitor, CPI-613, was analyzed.

Standard 3D co-culture assays as described in Example 2 were used toevaluate the cytotoxicity of the combination on tumor cells as well ascancer-associated fibroblasts.

As shown in FIGS. 15A-15C, there was greater than 50% killing of HCT-116colon cancer cells using 0.2, 0.8, 1.6, 3.1, 6.3 μM APX3330 whencombined with 100 and 75 μM CPI-613.

Example 5

In this Example, differences in gene expression of PDAC cell lines inresponse to APE1 siRNA knockdown were analyzed.

The effect of APE1 siRNA knockdowns were then analyzed in other PDAC lowpassage patient-derived cells. The effect of APE1 knockdown on thesegenes varied between the different patient lines, as shown in FIG.16A-16D, Pa02C, a cell line generated from liver metastasis of a PDACpatient, showed generally similar gene expression patterns to the Pa03Ccells, which were also isolated from PDAC liver metastasis. In Pa02Ccells, BCRP, COMMD7, ISYNA1, ITGA1, PRDX5, RAB3D, SIPA1 and TNFAIP2 alldemonstrated a decrease in expression, while NOTCH3 and PPIF weresignificantly increased following knockdown (FIG. 16A). Interestingly,while changes in expression of BCRP and NOTCH3 were significant, theywere in opposing directions to the changes seen in Pa03C cells.

Panc10.05 cells, derived from a primary PDAC tumor, exhibited similarresults to Pa03C cells, with eight of the 12 genes showing similarchanges in expression (FIG. 16B). COMMD7, ITGA1, RAB3D, SIPA1, TAPBP andTNFAIP2 show decrease, while BCRP and PPIF increased expression. Incontrast, CIRBP, ISYNA1, NOTCH3 and PRDX5 show no change in expressionin the Panc10.05 cells.

Panc198 cells, also originating from a primary tumor, produced the mostvaried results (FIG. 16C). No change in expression was seen for BCRP,CIRBP, ISYNA1, NOTCH3, PRDX5, PPIF, SIPA1 and TAPBP. COMMD7, ITGA1,RAB3D and TNFAIP2 all showed significantly decreased expression. COMMD7,ITGA1, RAB3D and TNFAIP2 were significantly changed in all fourpatient-derived cell lines tested (FIG. 16D).

Only six genes overlapped between the three analyses (TMEM45A, TMEM126A,TMEM154, COMMD7, ISYNA1 and TNFAIP2) (FIG. 10A), demonstrating that onlythese six genes were further affected as APE1 levels decreased. This wasan unexpected result, as a larger number of genes was expected to changefurther as APE1 levels decrease. Consequently, these results indicatethat the change in expression of most genes following APE1 knockdown isapparent when APE1 is at least reduced by 80% (based on the number ofAPE1 transcripts in the siAPE1 cells), and further reduction of APE1does not significantly increase or decrease most genes further. In thecase of several down-regulated genes, this was because initial APE1knockdown (detectable siAPE1 cells) already reduced their expression tonear zero, which meant further reduction of APE1 (undetectable siAPE1cells) had no effect on them.

DISCUSSION

BCRP (Breast cancer resistance protein)/ABCG2 is an ATP-binding cassette(ABC) transporter that is one of the proteins responsible for multidrugresistance of cancer cells. In PDAC, high BCRP expression corresponds tocarcinogenesis, tumor progression, early recurrence and poor survival.Several chemotherapeutic drugs are substrates for BCRP, which results intheir efflux from and reduced accumulation within the cells. An affecteddrug of particular interest is 5-fluorouracil (5-FU), which is currentlypart of the treatment regimen for PDAC patients. Therefore, thediscovery that APE1 knockdown affects BCRP expression is crucial whenlooking at future drug combinations to improve survival in PDAC.Combining APE1-targeted agents with 5-FU in tumors genetically similarto Pa02C should respond favorably to this combination due to reducedBCRP expression. A study in colon cancer stem cells indeed demonstrateddramatically increased cell killing when 5-FU and an inhibitor of APE1,APX3330, were used in vivo.

NOTCH3, a highly conserved member of the eponymous Notch signalingpathway, has been implicated in cell survival, proliferation,differentiation, development and homeostasis. Increased Notch3 proteinlevels have been identified as a prognostic marker for PDAC patients,and leads to increased tumor invasion, metastasis and shortened patientsurvival. Because of this, Notch3 has become a target for novel cancertherapies. γ-secretase inhibitors and DLL4-inhibiting antibodies bothtarget proteins upstream of Notch3, leading to the inhibition of theNotch signaling pathway. The identification of Notch3 as being affectedby APE1 opens up the possibility of combining APE1-targeted therapieswith these inhibitors to enhance (in Pa03C) or counteract (in Pa02C) theeffects of APE1 inhibition on NOTCH3 expression and function in PDAC.

Of the 10 other genes validated, four of them, COMMD7, ITGA1, RAB3D andTNFAIP2 showed decreased expression in all four patient cell lines (FIG.16D). COMMD7, ITGA1, RAB3D and TNFAIP2 have all been shown to beupregulated in various cancers including PDAC. While it cannot beassumed these changes will be universal in all PDAC samples, thisconsistency suggests that some of these genes could make promisingtargets or biomarkers for APE1-based therapy or combination therapiesthat potentially will be useful across multiple PDAC tumor subtypes andin other tumor types. Furthermore, these genes represent a fraction ofthe genes identified in this initial Example affected by APE1 knockdown.The identification of pathways formerly unassociated with APE1, as wellas known pathways exhibiting DEGs not previously linked with APE1, opensup novel targets for APE1-based combination therapies. In fact, initialexperiments targeting some of the identified pathways in combinationwith APE1 inhibition appear to be promising.

Example 6

Development of additional Ref-1 redox inhibitors based on APX3330 andrelated families of compounds has been undertaken. A number of analogshave been synthesized based on structure-activity relationship (SAR).Changes include alterations of the dimethoxybenzoquinone with anapthoquinone ring, modification of the carboxylic acid, carbon chain onthe double bond shortened, and substitution of the methyl group on thering structure with hydrogen or various halogens. APX3330 exists as acharged molecule at physiological pH; the addition of amide derivativesof carboxylic acid altered APX3330's physical properties. Also, thelipophilic carbon chain was shortened on the double bond, making the newcompounds less lipophilic. These changes resulted in new compounds(e.g., APX2009 and APX2014) that exhibited greater potency than APX3330during in vitro testing.

In this Example, the efficacies of analogs, APX2009 and APX2014, as wellas APX3330, were analyzed in 3D spheroid models of pancreatic cancer.

Co-Culture Model: To make 3D spheroid models, 3D tumor spheroid cultureswere grown in DMEM growth media supplemented with 5% FBS (Hyclone,Logan, Utah) and containing 3% Reduced Growth Factor Matrigel (RGF, BDBiosciences) in ultra low-attachment 96-well plates (Corning LifeSciences) as described in Sempere et al., Cancer biology & therapy 2011,12(3), 198-207; Arpin et al., Mol Cancer Ther 2016, 15(5), 794-805; andLogsdon et al., Mol Cancer Ther 2016, 15(11), 2722-2732. These spheroidcultures were grown with tumor cells alone or in the presence of CAFs(cancer-associated fibroblasts). To track growth throughout the culturetime and differentiate the cell types in the cultures, tumor cells werestably transduced with TdTomato (red channel), and CAFs were stablytransduced with EGFP (green channel). These modifications were performedin fresh, low-passage cells to preserve the heterogeneity and uniquegenetic characteristics of the patient cells, and growth rates weresimilar to uninfected cells. 3D spheroid cultures were analyzed on Days4, 8 and 12 after plating using Thermo ArrayScan high-content imagingsystem as described in Logsdon, Mol Cancer Ther 2016, 15(11), 2722-2732and Lindblom et al., Toxicologic pathology 2012, 40(1), 18-32. 3Dculture images were obtained by the ArrayScan system at 2.5×magnification with filters for TdTomato and EGFP. Quantification oftumor and CAF intensity and area was accomplished using 2D projectionsof these 3D images. Spheroids were treated on Days 4 and 8 followingArrayScan analysis/imaging. Confocal images of 3D spheroid cultures werecaptured with a confocal/two-photon Olympus Fluoview FV-1000 MPE system(Olympus Scientific Solutions America; Waltham, Mass.) at the IndianaCenter for Biological Microscopy facility (Indianapolis, Ind.) aspreviously described in Logsdon et al., Mol Cancer Ther 2016, 15(11),2722-2732.

These spheroid cultures were grown with Panc10.05 tumor cells alone orin the presence of CAFs (cancer-assoicated fibroblasts). Pa03C cellswere plated into 3D cultures alone or with CAF19 cells. Spheriods weretreated with increasing concentrations of napabucasin, vehicle (DMSO),APX3330 at 25 μM or 35 μM or combination of napabucasin and APX3330 ondays 4 and 8 following ArrayScan analysis/imaging. Tumor cell growth inthese spheroids was measured via fluorescence intensity (as well asarea, data not shown) on days 4, 8, and 12 after plating. 3D cultureswere treated with APX3330 (top row), APX2009 (middle row), or APX2014(bottom row) following measurements on days 4 and 8. Graphs are meanswith standard deviations of N=3.

As shown in FIG. 17, APX3330 and its second generation compounds,reduced cell growth, cell proliferation. Moreover, APX2009 and APX2014appeared as effective as APX3330 even when administered at a lowerdosage.

Example 7

In this Example, the combination of APX330 and the STAT3 inhibitor,napabucasin (BB1-608-STAT3 inhibitor), was analyzed for its tumorkilling ability in a patient-derived 3D spheroid model of pancreaticcancer as described in Example 6.

As shown in FIG. 18, the combination of APX3330 and napabucasin had asynergistic tumor killing effect.

Example 8

In this Example, combination therapy with APE1/Ref-1 inhibitors in aPDAC 3D co-culture model prepared as in Example 6 was analyzed.

Pa03C and Panc10.05 tumor cells were grown in 3D cultures in thepresence of CAFs. Spheroids were treated with either single agents,vehicle (DMSO) or combination of targeted agents on days 4 and 8 (blackarrows), and the intensity of tumor (red) and CAF (green) werequantified as described in Example 7 every 3-4 days in culture.

As shown in FIGS. 19A & 19B, the combination of APX3330 and napabucasinhad a synergistic tumor killing effect on pancreatic tumor cells.

Additionally, the combination of APX330, or its analog APX2009, and theSTAT3 inhibitor, napabucasin (BB1-608-STAT3 inhibitor), was analyzed forits tumor killing ability in the PDAC 3D co-culture model using the samemethodology. As shown in FIGS. 20A & 20B, both the combination ofAPX3330 and napabucasin and the combination of APX2009 and napabucasinhad a synergistic tumor killing effect as compared to any of the agentsalone.

Example 9

In this Example, the combination of APX330 and the STAT3 inhibitor,napabucasin, was analyzed for its tumor killing ability in a geneticPDAC model in vitro and in vivo.

In murine KPC (Kras^(LSL.G12D/+); Trp^(53R172H/+); Pdx1^(Cretg/+)) cellsderived from the GEMM, enhancement of Napa-induced cytotoxicity isobserved when APX3330 is added to the Napabucasin (FIG. 21A). Alamarblue proliferation-based assay demonstrates the syngergistic nature ofthe APX+Napabucasin combination after 3 days incubation with theseagents.

In a pilot study with a highly proliferative and aggressive in vivoco-culture model using patient derived tumor cells (Pa03C) and CAFsinjected together, the co-treatment of APX3330+Napa significantlyinhibited tumor growth 46% (FIG. 21B, p=0.012). Sub-lethal doses of thesingle agents were used in order to see the effect of the combinationtreatment, and the combination treatment was well tolerated in mice.Tumor volume is significantly reduced after two weeks of treatment.

Example 10

In this Example, the combination of APX330 and the CA9inhibitor,SLC-0111, was analyzed for its tumor killing ability in a 3Dco-culture pancreatic cancer tumor model prepared as described inExample 6.

Pa03C and 10.05 cells were plated into 3D cultures with CAF19 cells, andtumor cell growth in these spheroids was measured via fluorescenceintensity on days 4, 8, 12, and 16 after plating. 3D cultures weretreated with APX3330 and SLC-0111 following measurements on days 4, 8,and 12. Differences between groups were determined using Tukey'smultiple comparisons test: ***p<0.001 vs. DMSO; ++p<0.01 vs. APX3330;+++p<0.001 vs. APX3330; ̂̂<0.01 vs. SLC-0111; ̂̂̂<0.001 vs. SLC-0111.Graphs are means with standard deviations of N=3. Fluorescent images ofPa03C tumor cells (red channel) and CAFs (green channel) in thesespheroids were captured on day 12.

As shown in FIGS. 22A-22C, dual-targeting of CA9 and APE1 kills PDACtumors better than either agent alone.

Example 11

In this Example, combinations of APX330 and one other therapeutic agent(e.g., Bcl2 antagonist, HDAC 1 and 3 inhibitor, TKI inhibitor) wereanalyzed for their tumor killing abilities in a 3D co-culture pancreaticcancer tumor model prepared as described in Example 6.

Pa03C and Pancl0.05 tumor cells were grown in 3D cultures in thepresence of CAFs (cancer-associated fibroblasts). Spheroids were treatedwith either single agents, vehicle (DMSO) or combination of targetedagents on Days 4 and 8, and the area of tumor (red) and CAF (green) werequantified following 12 days in culture. Results are shown in FIGS.23A-23E.

Example 12

In this Example, combinations of APX330 and one of either the STAT3inhibitor, napabucasin, or the TCA cycle inhibitor, CPI-613, wereanalyzed for their tumor killing abilities in a 3D co-culture pancreaticcancer tumor model as described in Example 6.

Pa03C and Panc10.05 tumor cells were grown in 3D cultures in thepresence of CAFs. Spheroids were treated with either single agents,vehicle (DMSO) or combination of targeted agents on Days 4 and 8 (blackarrows), and the area of tumor (red) and CAF (green) were quantifiedfollowing 12 days in culture. Results are shown in FIGS. 24A-24C.

Example 13

In this Example, the combination therapy of APX3330 and STAT3 inhibitor,Ruxolitinib, was analyzed for inhibiting PDAC tumor growth.

Initially, it was confirmed that ruxolitinib blocks the phosphorylationof p-STAT3 (Y705) in the 3D co-culture model. Confirmation of inhibitionof STAT3 activation was done via immunoblotting for pSTAT3 Y705 residueafter 4 hours of Ruxolitinib treatment (12.5 μM) in the 3D assay 8-10days post plating. Total STAT3 protein is provided as a loading controland reference for the levels of STAT3 in both cell types. Representativewestern blot is shown from an n of 3. (see FIG. 26).

Using the 3D co-culture pancreatic cancer tumor model as described inExample 6, low passage patient-derived tumor cells, Pa03C, were grown in3D cultures in the presence and absence of CAFs. Spheroids were treatedwith Ruxolitinib alone and in combination with APX3330 (40 μM), and thearea of tumor (red channel) and CAF19#1 (green channel) were quantifiedfollowing 12 days in culture, n=4 but this is a representative plot.

As shown in FIG. 25, dual-targeting of Ref-1/APE1 and Jak/STAT signalinginhibited PDAC tumor growth in the 3D co-culture model.

Example 14

In this Example, the combination therapy of APX3330 and STAT3 inhibitor,Ruxolitinib, was analyzed for delaying tumor growth in a flankco-culture model.

Particularly, as shown in FIG. 27, in vivo efficacy experiments withpatient-derived Pa03C tumors showed a significant tumor growth delay invivo. Ruxolitinib (Rux) in combination with APX3330 also showed areduction in tumor volume in this aggressive co-culture model withpatient-derived line and CAFs.

Example 15

In this Example, the combination therapy of APX3330 and STAT3 inhibitor,Ruxolitinib, was analyzed to ensure that the treatment was not killingall CAFs in a co-culture model of PDAC in mice.

Immunohistochemistry (IHC) with vimentin as a marker for the CAFs wasused to ensure that the combination treatment was not killing all theCAFs in the co-culture model. Staining for vimentin was performed atsacrifice.

Methods for Immunohistochemistry staining of tumor tissue: Tissues werefixed overnight at room temperature in 10% NBF after which they weretransferred through graded concentrations of alcohol to xylene inside aLeica Automated Vacuum Tissue Processor. Tissues were embedded inparaffin before being cut into 5-mm thick sections, mounted ontopositively charged slides, and baked at 60° C. The slides were thendeparaffinized in xylene and rehydrated through graded alcohols towater. Antigen retrieval was performed by immersing the slides in aTarget Retrieval Solution (Dako) for 20 minutes at 90° C. (in a waterbath), cooling at room temperature for 10 minutes, washing in water, andthen proceeding with immunostaining. Slides were blocked with proteinblocking solution (Dako) for 30 minutes. All subsequent staining stepswere performed using the Dako FLEX SYSTEM on an automated Immunostainer;incubations were done at room temperature and Tris-buffered saline plus0.05% Tween 20, pH 7.4 (TBS—Dako Corp) was used for all washes anddiluents. The primary antibody was anti-mouse vimentin and p-STAT3.Control sections were treated with an isotype control using the sameconcentration as primary antibodies to verify the staining specificity.For whole slide digital imaging, the Aperio ScanScope CS system wasused. The system imaged all slides at 20×. The control and treatmentgroups were then evaluated for statistical differences. Results areshown in FIGS. 28A & 28B.

Treatment of the implanted tumors started on day 11 post implant.Particularly, the co-cultures implanted included 2.5×10⁶ tumor cells+/−5×10⁶ CAFs, providing a 1:2 ratio of tumor cell to CAF. The tumorshad an initial average tumor size of about 200 mm³. The mice were thenadministered either 50 mg/kg APX3330 BID in 4% Cr:EtOH, 50 mg/kg Rux SIDpm in 4% Cr:EtOH, or combinations of the agents. Treatment scheduleconsisted of treating for 5 days and then giving 2 days off treatmentuntil the tumors reached an average size of 2000 mm³. With no treatment,the mice reached an average tumor size of 2700 mm³ at day 26, with Ruxor APX3330 treatment alone, the mice reached an average size of 1750 m³at day 28, and with the combination therapy, the mice reached an averagesize of 1200 mm³ at day 31.

Example 16

In this Example, the anti-cancer efficacy of oxaliplatin with APX3330 incolon cancer orthotopic tumors was analyzed.

Immune competent mice were injected with mouse C26 colon cancer cells inthe caecum (FIG. 29A). Animals were treated with either oxaliplatin oroxaliplatin with APX3330 and tumor size determined compared to vehiclecontrols (FIG. 29B). There was a dramatic and significantly increasedtumor cell killing the in oxaliplatin and APX3330 treated mice comparedto the mice treated with oxaliplatin alone (FIGS. 29B & 29D).Additionally, APX3330 treatment alleviated oxaliplatin induced loss ofmyenteric neurons in the colon of the CRC mice (FIG. 29C).

Example 17

In this Example, the combination therapy of APX2014 and STAT3 inhibitor,napabucasin, was analyzed for its tumor killing ability in mouse coloncell line MC-38.

MC-38 cells (Yunhua Liu) were seeded in a 96-well tissue culture plateat 2000 cells/well in DMEM+10% FBS and grown overnight at 37° C., 5%CO₂. Media was exchanged with DMEM+5% FBS drug media containingNapabucasin (SELLECK CHEMICALS) serially diluted 1:2 in a 5-point spreadof 750 nM to 47 nM and spiked with APX2014 at EC30 (3.0 uM), or APX2014EC10 (2.0 uM), or alone for single agent. Cells were incubated for 72hours at 37° C., 5% CO₂. Media was exchanged with DMEM+5% FBS+10% Alamarblue fluorescent cell viability indicator (Invitrogen™) and incubated 4hours at 37° C., 5% CO₂ and then read on a fluorescent reader (Synergy™H4 BioTek). Results are shown in FIG. 30A. FIG. 30B shows APX2014 singleagent effect. Data shown is the average of 3 separate cytotoxicityassays; each assay normalized to media only control.

Example 18

In this Example, the combination therapy of APX3330 and PDH andalpha-KDH Metabolic inhibitor, CPI-613, was analyzed for its tumorkilling ability in human adenocarcinoma colon suspension cell lineColo-201.

Colo-201 (Yunhua Liu) was seeded in a 96-well tissue culture plate at2000 cells/well in RPMI+Sodium Pyruvate+10% FBS and grown overnight at37° C., 5% CO₂. 2× Drug Media RPMI+Sodium Pyruvate+5% FBS was added atdosages of APX3330 (Apexian) in a 5-point spread from 75 uM to 6.3 uMand spiked with CPI-613 (Apexbio Technology) at 75 uM, or 50 uM, oralone for single agent. Cells were incubated 72 hours at 37° C., 5% CO₂and then 10% Alamar blue fluorescent cell viability indicator(INVITROGEN™) was added directly to plate. Indicator was incubated 4hours at 37° C., 5% CO₂, and then read on a fluorescent reader (SYNERGY™H4 BioTek). FIG. 31A shows APX3330 and CPI-613 single agent effects.FIG. 31B shows APX3330 and CPI-613 synergistic combo effects. FIG. 31Cshows APX3330 and CPI-613 EC50 (CalcuSyn). FIG. 31D depicts Chou-TalalayIndex (CI) of dose combinations (CalcuSyn). FIG. 31E depicts synergisticdrug combinations (CalcuSyn) of APX3330 spiked with 50 uM CPI-613 or 75uM CPI-613. Drug combination synergy was observed at APX3330 dosages of75 uM and 50 uM when spiked with 50 uM CPI-613. Synergy was observed atall but one APX3330 dosage (6.3 uM) when spiked with 75 uM CPI-613. Datashown is the average of 3 separate cytotoxicity assays; each assaynormalized to media only control.

Example 19

In this Example, the combination therapy of APX3330 and PDH andalpha-KDH Metabolic inhibitor, CPI-613, was analyzed for its tumorkilling ability in human carcinoma colon cell line HCT-116.

HTC-116 (Yunhua Liu) was seeded in a 96-well tissue culture plate at2000 cells/well in DMEM+10% FBS and grown overnight at 37° C., 5% CO₂.Drug Media DMEM+5% FBS was added at dosages of APX3330 (Apexian) in a5-point spread from 75 uM to 6.3 uM and spiked with CPI-613 (ApexbioTechnology) at 75 uM, or 50 uM, or alone for single agent. Cells wereincubated for 72 hours at 37° C., 5% CO₂. Media was exchanged withDMEM+5% FBS+10% Alamar blue fluorescent cell viability indicator(INVITROGEN™) and incubated 4 hours at 37° C., 5% CO₂ and then read on afluorescent reader (SYNERGY™ H4 BioTek). FIG. 32A shows APX3330 andCPI-613 single agent effects. FIG. 32B shows APX3330 and CPI-613synergistic combo effects. FIG. 32C shows APX3330 and CPI-613 EC50(CalcuSyn). Figure d32D depicts Chou-Talalay Index (CI) of dosecombinations (CalcuSyn). FIG. 32E depicts synergistic drug combinations(CalcuSyn) of APX3330 spiked with 50 uM CPI-613 or 75 uM CPI-613. Drugcombination synergy was observed at APX3330 dosages of 75 uM and 50 uMwhen spiked with 50 uM CPI-613. Synergy was observed at all but oneAPX3330 dosage (6.3 uM) when spiked with 75 uM CPI-613. Data shown isthe average of 3 separate cytotoxicity assays; each assay normalized tomedia only control.

Example 20

In this Example, the combination therapy of APX3330 and PDH andalpha-KDH Metabolic inhibitor, CPI-613, was analyzed for its tumorkilling ability in human carcinoma colon cell line HCT-116.

HTC-116 (Yunhua Liu) was seeded in a 96-well tissue culture plate at2000 cells/well in DMEM+10% FBS and grown overnight at 37° C., 5% CO₂.Drug Media DMEM+5% FBS was added at dosages of APX3330 (Apexian) from100 uM to 0.4 uM in a 10-point spread and spiked with CPI-613 (ApexbioTechnology) at 100 uM, or 75 uM, or alone for single agent. Cells wereincubated for 72 hours at 37° C., 5% CO₂. Media was exchanged withDMEM+5% FBS+10% Alamar blue fluorescent cell viability indicator(INVITROGEN™) and incubated 4 hours at 37° C., 5% CO₂ and then read on afluorescent reader (SYNERGY™ H4 BioTek). FIG. 33A shows APX3330 andCPI-613 single agent effects. FIG. 33B shows APX3330 and CPI-613synergistic combo effects. FIG. 33C shows APX3330 and CPI-613 EC50(CalcuSyn). FIG. 33D depicts Chou-Talalay Index (CI) of dosecombinations (CalcuSyn). FIG. 33E depicts synergistic drug combinations(CalcuSyn) of APX3330 spiked with 100 uM CPI-613 or 75 uM CPI-613. Drugcombination synergy was observed at all APX3330 dosages when spiked with100 uM CPI-613. Synergy was observed at APX3330 dosages 100 uM-12.5 uMwhen spiked with 75 uM CPI-613. Data shown is the average of 3 separatecytotoxicity assays; each assay normalized to media only control.

Example 21

In this Example, the combination therapy of APX2014 and PDH andalpha-KDH Metabolic inhibitor, CPI-613, was analyzed for its tumorkilling ability in human carcinoma colon cell line HCT-116.

HTC-116 (Yunhua Liu) was seeded in a 96-well tissue culture plate at2000 cells/well in DMEM+10% FBS and grown overnight at 37° C., 5% CO₂.Drug Media DMEM+5% FBS was added at dosages of APX2014 (Apexian) in a5-point spread from 25 uM to 1.6 uM and spiked with CPI-613 (ApexbioTechnology) at 75 uM, or 50 uM, or alone for single agent. Cells wereincubated for 72 hours at 37° C., 5% CO₂. Media was exchanged withDMEM+5% FBS+10% Alamar blue fluorescent cell viability indicator(INVITROGEN™) and incubated 4 hours at 37° C., 5% CO₂ and then read on afluorescent reader (SYNERGY™ H4 BioTek). FIG. 34A shows APX2014 andCPI-613 single agent effects. FIG. 34B shows APX2014 and CPI-613synergistic combo effects. FIG. 34C shows APX2014 and CPI-613 EC50(CalcuSyn). FIG. 34D depicts Chou-Talalay Index (CI) of dosecombinations (CalcuSyn). FIG. 34E depicts synergistic drug combinations(CalcuSyn) of APX2014 spiked with 50 uM CPI-613 or 75 uM CPI-613. Drugcombination synergy could not be ascertained at APX2014 dosages whenspiked with 50 uM CPI-613. Synergy was observed at only one APX2014dosage (12.5 uM) when spiked with 75 uM CPI-613. Data shown is theaverage of 3 separate cytotoxicity assays; each assay normalized tomedia only control.

Example 22

In this Example, the combination therapy of APX3330 and GLS1 metabolicinhibitor, CB-839, was analyzed for its tumor killing ability in humancarcinoma colon cell line HCT-116.

HTC-116 (Yunhua Liu) was seeded in a 96-well tissue culture plate at2000 cells/well in DMEM+10% FBS and grown overnight at 37° C., 5% CO₂.Drug Media DMEM+5% FBS was added at dosages of APX3330 (Apexian) from100 uM to 0.4 uM in a 10-point spread and spiked with CB-839(Sigma-Aldrich) at 1000 nM, or 500 nM, or alone for single agent. Cellswere incubated for 72 hours at 37° C., 5% CO₂. Media was exchanged withDMEM+5% FBS+10% Alamar blue fluorescent cell viability indicator(INVITROGEN™) and incubated 4 hours at 37° C., 5% CO₂ and then read on afluorescent reader (SYNERGY™ H4 BioTek). FIG. 35A depicts APX3330 andCB-839 single agent effects. FIG. 35B depicts APX3330 and CB-839synergistic combo effects. FIG. 35C shows APX3330 and CB-839 EC50(CalcuSyn). FIG. 35D shows Chou-Talalay Index (CI) of dose combinations(CalcuSyn). FIG. 35E depicts synergistic drug combinations (CalcuSyn) ofAPX3330 spiked with 1000 nM CB-839 or 500 nM CB-839 (5-pt only). Drugcombination synergy was observed at APX3330 dosages 100 uM-25 uM whenspiked with 1000 nM. Synergy was observed at APX3330 dosages 100 uM-50uM when spiked with 500 nM CB-839. Data shown is the average of 3separate cytotoxicity assays; each assay normalized to media onlycontrol.

Example 23

In this Example, the combination therapy of APX3330 and cisplatin wasanalyzed for its tumor killing ability in the cisplatin resistantbladder cell line, BLCAb001.

The BLCAb001 (cisplatin resistant) cell line was treated with increasingconcentrations of APX2014 and cisplatin as single agents and incombination and assayed in a 96-hour viability assay. The concentrationsof APX2014 range from 6 mM-0.38 mM in combination with the indicatedcisplatin doses (FIG. 36A). Doses of 6 mM-3 mM were shown to besynergistic with combination indexes of >1.0. The concentrations ofCisplatin as a single agent range from 2.5 mM-0.04 mM (FIG. 36B).

Example 24

In this Example, the combination therapy of APX3330 and cisplatin wasanalyzed for its tumor killing ability in the cisplatin resistantbladder cell line, BLCAb002.

The BLCAb002 (cisplatin sensitive) cell line was treated with increasingconcentrations of APX2014 and cisplatin as single agents and incombination and assayed in a 96-hour viability assay. The concentrationsof APX2014 range from 6 mM-0.38 mM in combination with the indicatedcisplatin doses (FIG. 37A). Doses of 6 mM-1.5 mM were shown to besynergistic with combination indexes of >1.0. The concentrations ofcisplatin as a single agent range from 2.5 mM-0.04 mM (FIG. 37B).

Example 25

In this Example, the combination therapy of APX2014 and napabucasin(STAT3 inhibitor) was analyzed for its tumor killing ability in thebladder cell line, T24.

T24 bladder cancer cells were treated with increasing concentrations ofnapabucasin in the presence or absence of APX2014 (2.5 or 5.0 mM) for 72hours. The cells were then fixed, stained with methylene blue andrelative cell number was calculated via spectrophotometry. Results areshown in FIGS. 38A & 38B.

Example 26

In this Example, the combination therapy of APX2009 and napabucasin(STAT3 inhibitor) was analyzed for its tumor killing ability in thebladder cell line, T24.

T24 bladder cancer cells were treated with increasing concentrations ofnapabucasin in the presence or absence of APX2009 (2.5 or 5.0 mM; 3.5 or7 mM) for 72 hours. The cells were then fixed, stained with methyleneblue and relative cell number was calculated via spectrophotometry.Results are shown in FIGS. 39A & 39B.

Example 27

In this Example, the combination therapy of APX2014 and napabucasin(STAT3 inhibitor) was analyzed for its tumor killing ability in thebladder cell line, SCaBER.

SCaBER bladder cancer cells were treated with increasing concentrationsof napabucasin in the presence or absence of APX2014 (2.5 or 5.0 mM) for72 Hrs. The cells were then fixed, stained with methylene blue andrelative cell number was calculated via spectrophotometry. Results areshown in FIGS. 40A & 40B.

Example 28

In this Example, the combination therapy of APX2009 and napabucasin(STAT3 inhibitor) was analyzed for its tumor killing ability in thebladder cell line, SCaBER.

SCaBER bladder cancer cells were treated with increasing concentrationsof napabucasin in the presence or absence of APX2009 (2.5 or 5.0 mM; 3.5or 7 mM) for 72 hours. The cells were then fixed, stained with methyleneblue and relative cell number was calculated via spectrophotometry.Results are shown in FIGS. 41A & 41B.

Example 29

In this Example, the combination therapy of APX2009 and CA9 inhibitionwas analyzed for its tumor killing ability in pancreatic ductaladenocarcinoma (PDAC).

Cell Culture: Low-passage patient-derived PDAC cell lines and pancreaticcancer-associated fibroblasts used in this Example were received fromDr. Anirban Maitra (The Johns Hopkins University) and maintained asdescribed in Logsdon et al. (2016 Mol Cancer Ther 15(11):2722-2732),Fishel et al. (2011 Mol Cancer Ther 10(9):1698-1708), Su et al. (2011Biochem 50:82-92), and Zhang et al. (2013 Biochem 52(17):2955-2966).Cells were submitted for STR analysis (CellCheck with IDEXX BioResearch)and were tested regularly for mycoplasma contamination. Cell lines werepassaged fewer than 12 times before resuscitating fresh stocks. Hypoxicconditions in monolayer experiments were generated in a Ruskinn Invivo₂200 hypoxia work station (Baker Ruskinn; Sanford, Me.) at 0.2% oxygen.Cell proliferation and viability in monolayer cultures was measured withalamarBlue assay. Growth of 3-dimensional tumor spheroid cultures wasperformed and quantified as described in Logsdon et al. (2016 Mol CancerTher 15(11):2722-2732), Sempere et al. (2011 Cancer Biol & Ther12(3):198-207), and Arpin era al. (2016 Mol Cancer Ther 15(5):794-805).

Western Blot Analysis: Immunoblotting was performed using antibodies forAPE1/Ref-1 (Novus Biologicals; Littleton, Colo.), CA9 (Santa Cruz;Dallas, Tex.), Actin (NeoMarkers; Fremont, Calif.), and Vinculin (Sigma;St. Louis, Mo.). All samples were processed and run in parallel asdescribed in Logsdon et al. (2016 Mol Cancer Ther 15(11):2722-2732) andFishel et al. (2011 Mol Cancer Ther 10(9):1698-1708).

siRNA Transfections: PDAC cells were transfected with siRNA aspreviously described in Logsdon et al. (2016 Mol Cancer Ther15(11):2722-2732), Fishel et al. (2011 Mol Cancer Ther 10(9):1698-1708),and Arpin era al. (2016 Mol Cancer Ther 15(5):794-805). siRNAs used werescrambled control and siAPE1/Ref-1 (SEQ ID NOS:1-3), as well as OriGene(Rockville, Md.) Trisilencer siCA9.

Inhibitors: Small molecule inhibitors were prepared and used aspreviously described in Logsdon et al. (2016 Mol Cancer Ther15(11):2722-2732), Fishel et al. (2011 Mol Cancer Ther 10(9):1698-1708),Su et al. (2011 Biochem 50:82-92), and Zhang et al. (2013 Biochem52(17):2955-2966). APE1/Ref-1 redox signaling was inhibited usingAPX3330, APX2009, and APX2014 (Apexian Pharmaceuticals; Indianapolis,Ind.), with RN7-58 (Apexian Pharmaceuticals) used as a negative controlthat, although structurally similar, does not inhibit APE1/Ref-1 redoxsignaling activity (Shah et al. 2017 NPJ Precision Oncology 1; Kelley etal., 2017 Neural Regen Res 12(1):72-74; Kelley et al., 2016 J PharmacolExp Ther 359(2):300-039; Fishel et al., 2011 Mol Cancer Ther10(9):1698-1708). CA9 inhibition was accomplished with SLC-0111 andFC12-531A (Logsdon et al. (2016 Mol Cancer Ther 15(11):2722-2732);Supuran et al., 2015 Expert Opinion on Drug Discovery 10(6):591-597;Chen et al., 2017 Am Soc Hematology; Koenig et al., 2017 ExperimentalHematology 53, S88; Fishel et al. (2011 Mol Cancer Ther10(9):1698-1708). All of these compounds have been administered in micewith minimal toxicity, though ongoing studies are evaluating theirsafety and efficacy alone and in combination with other agents in vivo.

ChIP Assay: Chromatin Immunoprecipitation (ChIP) was performed using theMagna ChIP kit (Millipore). Immunoprecipitation (IP) was performed usingpolyclonal antibodies for HIF1α (Novus) or Rabbit IgG control(Millipore). Binding to the HIF-1-Binding Site (HBS) in the CA9 promoterwas measured via qPCR using SYBR Green master mix (Applied Biosystems)in a CFX96 Real-Time System (Bio-Rad). Primer sequences used for ChIPqPCR were: CA9 HBS-Fwd (5′-CTCACTCCACCCCCATCCTA-3′)(SEQ ID NO:32) andCA9 HBS-Rev (5′-GGACCGAGGGAGACAACTAG-3′) (SEQ ID NO:33). 1% of thecross-linked DNA from each sample was evaluated (without IP) as acontrol to normalize the qPCR signal across samples (Input).

pH Assay: Intracellular pH was measured with pHrodo Red AM IntracellularpH Indicator (LifeTech) as described in Logsdon et al. (2016 Mol CancerTher 15(11):2722-2732). Fluorescent images of pHrodo Red AM-exposedcells were captured with a confocal/two-photon Olympus Fluoview FV-1000MPE system (Olympus Scientific Solutions America; Waltham, Mass.) at theIndiana Center for Biological Microscopy facility (Indianapolis, Ind.)as previously described in Logsdon et al. (2016 Mol Cancer Ther15(11):2722-2732).

qRT-PCR: mRNA levels were measured using qRT-PCR as previously describedin Logsdon et al. (2016 Mol Cancer Ther 15(11):2722-2732), Fishel et al.(2011 Mol Cancer Ther 10(9):1698-1708), Fischer et al. (2015 J Biol Chem290(5):3057-3068). The comparative Ct method was used to quantitate mRNAlevels using RPLPO and B2M as reference genes. The primers for CA9,RPLPO, and B2M are commercially available (Applied Biosystems).Experiments were performed in triplicate for each sample.

Immunohistochemistry (IHC): 3D spheroid cultures were collected on day12 after plating, fixed with 4% paraformaldehyde (PFA) (ElectronMicroscopy Sciences; Hatfield, Pa.), and permeabilized with 70% ethanol.Fixed/permeabilized 3D cultures were solidified in HistoGel (LifeTech).HistoGel plugs were paraffin embedded and slides were prepared by thelaboratory of Dr. Keith Condon (Indiana University School of Medicine;Indianapolis, Ind.). Samples were stained with the specified antibodiesby the Indiana University School of Medicine ResearchImmunohistochemistry Facility (Indianapolis, Ind.).

Statistical Analysis: Comparisons in experiments with more than twogroups were analyzed with post-hoc Multiple Comparisons Tests (Tukey,Dunnett, or Sidak as appropriate) Logsdon et al. (2016 Mol Cancer Ther15(11):2722-2732), McHugh (2011 Biochem 21(3):203-209), and Stevens etal. (2017 PloS One 12(4):e0176124). Differences between groups wereconsidered significant if p<0.05. Statistical analyses were performedwith Microsoft Excel and Prism (Version 6.0f, Copyright©2014 GraphPadSoftware Inc. La Jolla, Calif.).

Results

APE1/Ref-1-HIF-1-CA9 Signaling Axis in PDAC Cells

To characterize the response of different PDAC patient lines toAPE1/Ref-1 and/or CA9 inhibition, the effects of inhibition of CA9 viasmall molecule inhibitor, SLC-0111, or siRNA were evaluated inpatient-derived cells. Although CA9 is well-established as ahypoxia-regulated enzyme, the level of CA9 expression induced underhypoxic conditions is variable between patient lines. Therefore, therelative CA9 expression in a selection of low-passage patient-derivedPDAC cell lines (10.05, Pa02C, and Pa03C) was determined following 24hrs exposure to 0.2% oxygen, as compared to cells incubated in normoxicconditions. Hypoxia exposure significantly induced CA9 protein levels inall cell lines (2.5-21.5-fold), including cancer-associated fibroblastcells (CAF19) (FIG. 42A). However, CA9 was most strongly induced in the10.05 cells (21.5-fold over normoxia), and Pa03C cells had the lowestlevels of hypoxia-induced CA9 protein (2.5-fold over normoxia). Notably,APE1/Ref-1 expression was not significantly affected by hypoxia exposurein these cells. The majority of mechanistic experiments were evaluatedin 10.05 cells because of their robust CA9 induction and were repeatedin the CA9-weak Pa03C cells to confirm and compare responses.

The efficacy of SLC-0111, a CA9 inhibitor that has recently completed aPhase I clinical trial, was evaluated in different PDAC cell lines underhypoxic conditions for comparison. While all three of thepatient-derived PDAC cell lines tested had LC₅₀s for SLC-0111 below 100μM during hypoxia exposure (FIG. 42B), the most sensitive cell line was10.05, which induces CA9 expression to the highest level followinghypoxia exposure (FIG. 42A). In fact, CA9 protein induction underhypoxia was inversely correlated with SLC-0111 LC₅₀ under hypoxia in thecell lines tested (R2>0.99) (FIG. 42B), indicating that increased CA9induction may predict increased sensitivity to CA9 inhibition in PDACcells.

Induction of CA9 in pancreatic cancer cells grown in monolayer versus 3Dtumor spheroids were compared. Following exposure to 0.2% hypoxia usinga hypoxic chamber in the 10.05 monolayer cultures, CA9 was induced˜21-fold (FIGS. 42A and 42C). Using the 3D tumor spheroid system withand without CAFs, CA9 expression was further increased 2.5 and 6.2-fold,respectively, over hypoxic monolayer cultures despite these spheroidcultures being grown in normoxic conditions (FIG. 42C). Based on therelevance of the 3D culture model, the effects of inhibition of CA9 andAPE1/Ref-1 were further evaluated in this system.

Knockdown of APE1/Ref-1 and CA9 expression was evaluated in 3D spheroidcultures to determine whether the growth and survival of PDAC cells inthis relevant microenvironment was dependent upon CA9 and APE1/Ref-1expression. Spheroids were collected on day 8 to confirm the continuedknockdown of CA9 and APE1. Each siRNA significantly reduced theexpression of its target gene/enzyme product, confirming the continuedknockdown of these enzymes throughout the duration of the 3D cultures.APE1/Ref-1 knockdown also decreased CA9 expression to a similar extentto that seen in siCA9 cultures (FIG. 42D FIG. 1D). Reduced levels ofAPE1/Ref-1 and/or CA9 significantly slowed 3D tumor spheroid growth by˜50-80% (p<0.001) as measured by fluorescence intensity and area (FIGS.42E and 42F). These results confirm the importance of APE1/Ref-1 and CA9expression in PDAC tumor growth. Additionally, APE1/Ref-1 knockdownslowed 3D tumor spheroid growth significantly more than CA9 knockdown,which indicated that inhibition of CA9 alone may not be as efficient atattenuating PDAC tumor growth as dual-targeting these enzymes.

Inhibition of APE1/Ref-1 redox signaling decreased HIF-1-mediated CA9transcription and subsequent expression (FIG. 42D). To determine whetherthis was the result of a direct effect on HIF1α binding to the CA9promoter, a chromatin immunoprecipitation (ChIP) assay was performed toinvestigate HIF-1-DNA interactions. 10.05 cells were treated with theAPE1/Ref-1 redox signaling inhibitor APX3330 and exposed to 0.2% O₂ for12 hrs. Immunoprecipitations (IPs) of HIF1α demonstrated a 4.3-foldincrease in HIF1α binding to the HIF-1-Binding Site (HBS) in the CA9promoter under hypoxic conditions, which was decreased by −60% in cellstreated with APX3330 (FIGS. 42G and 42H). These data demonstrate thatHIF1α interactions with the CA9 promoter were induced by hypoxia, andthat these hypoxia-induced interactions were attenuated by APE1/Ref-1redox signaling inhibition, providing further confirmation of themechanism by which APE1/Ref-1 redox signaling regulates HIF-1-mediatedCA9 transcription under hypoxic conditions.

Blockade of CA9 Via APE1/Ref-1 or CA9 Inhibition

To determine target selectivity, analogs of APX3330, APX2009 andAPX2014, and an analog of SLC-0111, FC12-531A, were used. All of whichdemonstrated improved cytotoxicity over their parent compounds underhypoxic conditions (Table 7).

Hypoxia-induced CA9 mRNA and protein levels were evaluated in 10.05cells following treatment with APX3330, APX2009, APX2014, and theinactive analog RN7-58. Inhibition of APE1/Ref-1 with all threeinhibitors resulted in concentration-dependent decreases inhypoxia-induced CA9 mRNA and protein levels, with 10-fold less requiredfor APX2009 and APX2014 vs. APX3330 (FIGS. 43A and 43B), indicating thatthese analogs were more potent inhibitors of APE1/Ref-1 redox signalingthan APX3330. The inactive analog (RN7-58) did not affecthypoxia-induced CA9 expression even at 100 μM, further confirming theselective contribution of APE1/Ref-1 redox signaling activity to theeffects seen with the other compounds.

The effect of APE1/Ref-1 redox inhibition on CA9 protein expression wasalso measured in 3D tumor spheroids. 10.05 cells were grown in 3Dcultures for 12 days and treated on days 4 and 8 with APX3330, APX2009and APX2014, or the inactive analog (RN7-58). APE1/Ref-1 redoxinhibition significantly decreased the expression of CA9 protein in 3Dtumor cultures in a concentration-dependent manner (FIG. 43C).Importantly, the APX2009 and APX2014 APE1/Ref-1 inhibitors required10-fold less of the concentration compared to APX3330 to attenuate CA9expression in the spheroid cultures, further validating the potency ofthese compounds. The inactive analog (RN7-58) did not affect CA9expression in PDAC spheroid cultures, once again corroborating thespecificity of the effects of the APE1/Ref-1 redox signaling inhibitorson HIF1α activity.

CA9 expression is important for tumor cell growth, and CA9 functions bystabilizing intracellular pH to counteract the acidification that occursin response to metabolic changes under hypoxic conditions. As afunctional marker for CA9 activity, the effects of CA9 on intracellularpH were evaluated. Hypoxia exposure (0.2% O₂ for 48 hrs) did notsignificantly affect intracellular pH in 10.05 cells (FIGS. 43D and43E), indicating that these cells compensate for the effects of hypoxiaon pH. However, when CA9 expression was reduced via siRNA, the resultwas a significant decrease in intracellular pH in hypoxia-exposed cells,as measured by increased fluorescence of the pH-sensitive pHrodo Red AMdye (FIGS. 43D and 43E). These data support the conclusion that CA9 isresponsible for regulating pH in these cells.

APX3330 and SLC-0111 did not affect intracellular pH as single-agents atconcentrations up to 50 μM APX3330 or 100 μM SLC-0111, instead requiringthe combination of both compounds to acidify hypoxic PDAC cells.Therefore, the APX3330 analogs, APX2009 and APX2014, were used todetermine whether APE1/Ref-1 redox inhibition alone can shiftintracellular pH in hypoxic PDAC cells given a sufficiently potentinhibitor. Treatment with either 8 μM APX2009 or 5 μM APX2014 aloneresulted in a significant increase in fluorescence (normalized to cellsurvival), indicating decreased intracellular pH with single-agentAPE1/Ref-1 redox signaling inhibition (FIGS. 2D-2E). Due to the decreasein CA9 expression following APE1/Ref-1 inhibition, these data show thatAPE1/Ref-1 redox signaling inhibition alone was sufficient to acidifycells. Taken together, the data in FIGS. 43D and 43E indicated thatdecreases in CA9 expression via either siRNA or APE1/Ref-1 redoxinhibition resulted in intracellular acidification in hypoxic PDACcells.

Following these mechanistic results, the effects of the APE1/Ref-1 redoxsignaling inhibitors, APX2009 and APX2014, were compared to APX3330 in3D PDAC tumor+CAF co-cultures using 10.05 (FIG. 43F) or Pa03C (FIG. 43G)tumor cells. Each of these analogs exhibited LC₅₀s between 4-50-foldlower than APX3330 in this 3D tumor spheroid model (Table 7), suggestingthat they have improved potency in their tumor growth-inhibitory effectscompared to APX3330. Similarly, a more potent analog of CA9 inhibitor,SLC-0111, FC12-531A exhibited LC₅₀s˜15-fold lower than SLC-0111 in this3D tumor spheroid model (FIGS. 43H and 43I, Table 7), demonstratingimproved potency in its tumor growth-inhibitory effects over SLC-0111.Surprisingly, as shown in Table 7, APX2009 and APX2014 were more potentas single agents compared to the parent compound, APX3330. Incombination studies, the analogs, APX2009 and APX2014, could be used atmuch lower concentrations to achieve a better combinatory effect.

TABLE 7 Panc10.05 Pa03C Monolayer (Hypoxia) APX3330 40.3 50.2 APX20094.9 6.7 APX2014 1.3 3.5 SLC-0111 63.9 90.8 FC12-531A 1.4 1.1 3D CulturesTumor Alone APX3330 44.5 37.9 APX2009 9.4 6.9 APX2014 0.3 1.1 SLC-011164.0 51.9 FC12-531A 4.8 3.0 Tumor + CAFs APX3330 57.9 41.6 APX2009 13.08.4 APX2014 1.2 2.4 SLC-0111 70.8 64.1 FC12-531A 4.9 3.8 CAFs APX333059.4 57.3 APX2009 14.1 13.1 APX2014 6.3 7.1 SLC-0111 98.2 97.0 FC12-531A4.6 5.3 *N = 3 **All concentrations are μM ****3D culture datacalculated from D12 curves

Effect of Dual-Targeting APE1/Ref-1 and CA9 in 3D Cultures

Characterization of 3D spheroid cultures was performed using H&Estaining, Vimentin (to detect CAFs within the co-cultures), and Masson'sTrichrome (FIGS. 44A-44C). These data indicated that the tumor cellswere more densely packed than the CAFs in the 3D co-cultures, and theMasson's Trichrome stain indicated that the CAFs deposit extracellularmatrix (ECM) components such as collagen, validating this model asrepresentative of the fibrotic tumors seen in PDAC patients. Notably,APE1/Ref-1 staining was primarily nuclear and appeared to be uniform intumor cells throughout the cultures in all 3D cultures tested (FIG.44D). Furthermore, the hypoxia markers CA9 and Glucose Transporter 1(Glut-1) showed positivity in distinct regions (FIGS. 44E and 44F),indicating differential zones of hypoxia within the spheroid cultures.These data demonstrated that culturing PDAC cells in this 3D tumorspheroid model resulted in hypoxic cells that expressed CA9 without theneed for external induction of low-oxygen conditions.

APE1/Ref-1 Redox Signaling Inhibition Sensitized 3D PDAC Tumor Spheroidsto CA9 Inhibition with Second-Generation Inhibitors

Combination treatment with APX3330 and SLC-0111 significantly attenuatedtumor cell growth with minimal effects on the CAFs in the spheroidco-cultures at Day 12 of co-culture in 3D co-cultures containing bothPDAC tumor cells and CAFs. To characterize the growth inhibitory effectsof the compounds over time and determine the optimal regimen, the timein culture was extended to 16 days and assayed for growth after eachtreatment. The combination therapy was more effective than monotherapyin both patient-derived cell lines. SLC-0111 was also combined withAPX2009 at 10 μM or APX2014 at 0.6 μM in 3D co-cultures, which showedsimilar results as with APX3330 at 50 μM.

To further determine the effects of CA9 inhibition and APE1/Ref-1inhibition in PDAC cells, the SLC-0111 analog, FC12-531A, was employed,which showed the same trend as SLC-0111 in the tumor cells in thismodel, but with substantially lower concentrations needed to achievesimilar effects (3 μM FC12-531A vs. 50 μM SLC-0111). Specifically, 3 μMFC12-531A monotherapy significantly affected tumor cell growth in Pa03Cco-cultures, but not in 10.05 co-cultures, and FC12-531A significantlyenhanced the effects of APX3330, APX2009, and APX2014 on 3D tumor cellgrowth in both 10.05 and Pa03C co-cultures (FIGS. 45A-45R). These datavalidate results showing enhanced PDAC tumor cell killing withdual-targeting of APE1/Ref-1 redox signaling and CA9 activity whilemoving forward with novel inhibitors that have improved potency,allowing for nanomolar-to-low-micromolar concentrations of each drugused with the most potent combination (0.6 μM APX2014+3 μM FC12-531A,FIGS. 4M-4R).

These results demonstrate an arm of the APE1/Ref-1 regulatory nodeconnecting APE1/Ref-1 redox signaling through HIF-1-mediatedtranscription to CA9 expression and activity (FIG. 46). Specifically,the results presented herein expand the significance of this signalingaxis using novel analogs of clinical compounds to dual-target APE1/Ref-1redox signaling and CA9 activity in 3D PDAC tumor cultures, resulting inenhanced killing of tumor cells in spheroid co-cultures. The resultspresented herein also show for the first time that hypoxia-inducedinteractions between HIF-1 and the promoter of one of its majortranscriptional targets are decreased following APE1/Ref-1 redoxsignaling inhibition (FIG. 42C), providing a key bridge in theunderstanding of APE1/Ref-1 contributions to HIF-1-mediatedtranscription.

1. A combination therapy comprising an Apurinic/ApyrimidinicEndonuclease/reduction-oxidation (redox) Factor-1 (APE1/Ref-1)inhibitor, wherein the APE1/Ref-1 inhibitor inhibits the redox functionof APE1/Ref-1 and a second therapeutic agent, wherein the secondtherapeutic agent is selected from the group consisting of a Bcl-2inhibitor, a PTEN inhibitor, a WNT/β-catenin inhibitor, a pyruvatedehydrogenase (PDH) inhibitor, a α-ketoglutarate dehydrogenaseinhibitor, a Notch3 inhibitor, a photodynamic therapy (PDT), andcombinations thereof.
 2. The combination therapy as set forth in claim 1wherein the APE1/Ref-1 inhibitor is selected from the group consistingof 5-(2,3-dimethoxy-6-methyl 1,4-benzoquinoyl)]-2-nonyl-2-propenoic acid(APX3330),[(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-N,N-diethylpentanamide](APX2009),(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronapthalen-2-yl)methylidene]-N-methoxypentanamide](APX2014)and combinations thereof.
 3. The combination therapy as set forth inclaim 1 wherein the second therapeutic agent is selected from the groupconsisting of doxorubicin, endostatin, 5-fluorouracil (5-FU),bortezomib, ispinesib mesylate, SN-38, topotecan, paclitaxel, bryostatin1, trametinib, LAQ824, vinblastine, BEZ235, panobinostat, methotrexate,temsirolimus, FK866, afatinib, tozasertib, irinotecan, GSK2126458,CPI-613, γ-secretase inhibitors, DLL4-inhibiting antibodies, andcombinations thereof.
 4. A combination therapy comprising(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronapthalen-2-yl)methylidene]-N-methoxypentanamide](APX2014), wherein the APE1/Ref-1 inhibitor inhibits the redox functionof APE1/Ref-1, and a second therapeutic agent.
 5. The combinationtherapy as set forth in claim 1 wherein the second therapeutic agent isselected from the group consisting of a carbonic anhydrase IX (CA9)inhibitor, signal transduce and activator of transcription 3 (STAT3)inhibitor, platinating agent, and combinations thereof.
 6. Thecombination therapy as set forth in claim 5, wherein the secondtherapeutic agent is a CA9 inhibitor selected from the group consistingSLC-0111, FC13-555A, FC12-531A, and combinations thereof.
 7. (canceled)8. The combination therapy as set forth in claim 5, wherein the secondtherapeutic agent is a STAT3 inhibitor selected from the groupconsisting of napabucasin, ruxolitinib, and combinations thereof. 9.(canceled)
 10. The combination therapy as set forth in claim 5, whereinthe second therapeutic agent is a platinating agent selected from thegroup consisting of cisplatin, oxaliplatin, carboplatin, andcombinations thereof.
 11. (canceled)
 12. The method as set forth inclaim 24, wherein the cancer is selected from the group consisting ofprostate, pancreatic, pancreatic ductal adenocarcinoma, cervical,ovarian, osteosarcoma, germ cell tumor, colon/colorectal, bladder, headand neck, gastric/gastro-esophageal, neuroectodermal tumors,rhabdomyosarcomas, pancreaticobiliary, adult gliomas, non-small celllung, hepatocellular, multiple myeloma, esophageal, breast, pediatricependymoma, and melanoma.
 13. The method as set forth in claim 24,wherein the cancer is colon cancer, and the combination therapycomprises an APE1/Ref-1 inhibitor being selected from the groupconsisting of 5-(2,3-dimethoxy-6-methyl1,4-benzoquinoyl)]-2-nonyl-2-propenoic acid (APX3330),[(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-N,N-diethylpentanamide](APX2009), and combinations thereof, and a second therapeutic agentbeing selected from the group consisting of doxorubicin, 5-fluorouracil(5-FU), CPI-613, oxaliplatin, napabucasin, CP-839, and combinationsthereof.
 14. The method as set forth in claim 24, wherein the cancer isleukemia, and the combination therapy comprises an APE1/Ref-1 inhibitorbeing selected from the group consisting of 5-(2,3-dimethoxy-6-methyl1,4-benzoquinoyl)]-2-nonyl-2-propenoic acid (APX3330),[(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-N,N-diethylpentanamide](APX2009), and combinations thereof, and a second therapeutic agentbeing retinoic acid.
 15. The method as set forth in claim 24, whereinthe cancer is malignant peripheral nerve sheath tumors, and thecombination therapy comprises an APE1/Ref-1 inhibitor being selectedfrom the group consisting of 5-(2,3-dimethoxy-6-methyl1,4-benzoquinoyl)]-2-nonyl-2-propenoic acid (APX3330),[(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-N,N-diethylpentanamide](APX2009), and combinations thereof, and a second therapeutic agentbeing a survivin inhibitor.
 16. The method as set forth in claim 24,wherein the cancer is non-small cell lung carcinoma, and the combinationtherapy comprises an APE1/Ref-1 inhibitor being selected from the groupconsisting of 5-(2,3-dimethoxy-6-methyl1,4-benzoquinoyl)]-2-nonyl-2-propenoic acid (APX3330),[(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-N,N-diethylpentanamide](APX2009), and combinations thereof, and a second therapeutic agentbeing selected from the group consisting of a Bcl-2 inhibitor, aphotodynamic therapy, and combinations thereof.
 17. The method as setforth in claim 24, wherein the cancer is prostate cancer, and thecombination therapy comprises an APE1/Ref-1 inhibitor being selectedfrom the group consisting of 5-(2,3-dimethoxy-6-methyl1,4-benzoquinoyl)]-2-nonyl-2-propenoic acid (APX3330),[(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-N,N-diethylpentanamide](APX2009), and combinations thereof, and a second therapeutic agentbeing a survivin inhibitor.
 18. (canceled)
 19. The method as set forthin claim 25, wherein the retinal disease is selected from the groupconsisting of choroidal neovascularization (CNV), age-related maculardegeneration (AMD), retinopathy of prematurity (ROP), diabeticretinopathy (DR)), and ischemic retinopathy.
 20. (canceled) 21.(canceled)
 22. (canceled)
 23. (canceled)
 24. A method of treating cancerin a subject in need thereof, the method comprising administering to thesubject the combination therapy of claim
 1. 25. A method of treatingretinal disease in a subject in need thereof, the method comprisingadministering to the subject the combination therapy of claim
 1. 26. Amethod of treating a disease in a subject in need thereof, the methodcomprising administering to the subject the combination therapy of claim1, wherein the disease is selected from the group consisting ofcardiovascular disease, bacterial infection, gastric inflammatorydisorder, and neurodegenerative disease.
 27. A method of treatingchemotherapy-induced peripheral neuropathy (CIPN) in a subject in needthereof, the method comprising administering to the subject thecombination therapy of claim
 1. 28. The method as set forth in claim 27,wherein the combination therapy comprises an APE1/Ref-1 inhibitor beingselected from the group consisting of 5-(2,3-dimethoxy-6-methyl1,4-benzoquinoyl)]-2-nonyl-2-propenoic acid (APX3330),[(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronaphthalen-2-yl)methylidene]-N,N-diethylpentanamide](APX2009),(2E)-2-[(3-methoxy-1,4-dioxo-1,4-dihydronapthalen-2-yl)methylidene]-N-methoxypentanamide](APX2014) and combinations thereof, and a second therapeutic agent beinga platinating agent selected from the group consisting of cisplatin,oxaliplatin, carboplatin, and combinations thereof.